Robert M. Morgenthau, a courtly Knickerbocker patrician who waged war on crime for more than four decades as the chief federal prosecutor for Southern New York State and as Manhattan’s longest-serving district attorney, died on Sunday in Manhattan. He was 99.

Mr. Morgenthau’s wife, Lucinda Franks, said he died at Lenox Hill Hospital after a short illness.

In an era of notorious Wall Street chicanery and often dangerous streets, Mr. Morgenthau was the bane of mobsters, crooked politicians and corporate greed; a public avenger to killers, rapists and drug dealers; and a confidant of mayors and governors, who came and went while he stayed on — for nearly nine years in the 1960s as the United States attorney for the Southern District of New York and for 35 more as Gotham’s aristocratic Mr. District Attorney.

For a Morgenthau — the scion of a family steeped in wealth, privilege and public service — he was strangely awkward, a wooden speaker who seemed painfully shy on the stump. His grandfather had been an ambassador in President Woodrow Wilson’s day, and his father was President Franklin D. Roosevelt’s treasury secretary. His own early political forays, two runs for governor of New York, ended disastrously.

But from Jan. 1, 1975, when he took over from an interim successor to the legendary district attorney Frank S. Hogan, to Dec. 31, 2009, when he finally gave up his office in the old Criminal Courts Building on the edge of Chinatown, Mr. Morgenthau was the face of justice in Manhattan, a liberal Democrat elected nine times in succession, usually by landslides and with the endorsement of virtually all the political parties.

He presided over a battalion of 500 lawyers, a $75 million budget and a torrent of cases every year that fixed the fates of accused stock manipulators, extortionists, murderers, muggers, wife-beaters and sexual predators, and in turn helped to shape the quality of life for millions in a city of vast riches and untold hardships.

While he rarely went to court himself, Mr. Morgenthau, by his own count, supervised a total of 3.5 million cases over the years. Many of them were run-of-the-mill drug busts, but there were also highly publicized trials, like those of the subway vigilante Bernard Goetz; the Central Park “preppy” killer, Robert Chambers; and John Lennon’s assassin, Mark David Chapman.

His victories included the 2005 conviction of L. Dennis Kozlowski, chief executive of Tyco International, whose $6,000 shower curtains and a $2 million birthday party for his wife on the Mediterranean island of Sardinia came to symbolize corporate greed. Found guilty of misappropriating more than $100 million from his company, Mr. Kozlowski was sentenced to eight to 25 years, although he won parole in 2014.

In a bizarre case, Mr. Morgenthau may have been the only prosecutor in history to convict a mother and son for murder without a body or a witness. The defendants, Sante and Kenneth Kimes, were accused of a scheme in 1998 to assume the identity of their landlady, the 82-year-old socialite Irene Silverman, and take over her $7.7 million Manhattan mansion.

Her body was never found, but they were convicted of her murder and scores of other charges in 2000, partly on the basis of Sante Kimes’s notebooks detailing the plot and notes by the victim expressing fear of her lodgers. Sante Kimes denied everything, but Kenneth confessed later that his mother had used a stun gun on the victim and that he had then strangled her, stuffed the body in a bag and left it in a dumpster in Hoboken, N.J.

Mr. Morgenthau’s pursuit of crime sometimes took him beyond Manhattan. In 2004, he won a bribery-conspiracy case against State Senator Guy J. Velella, a Republican whose district lay entirely outside Manhattan, in the Bronx and Westchester County. Prosecutors using surveying equipment showed that one crime scene was within 500 yards of Manhattan, and argued successfully that it fell within their jurisdiction.

Federal prosecutors said Mr. Morgenthau also did not respect jurisdictional lines when he followed the money trails in white-collar crimes to Paraguay, Iran, the Cayman Islands and Belgium. Two weeks before he retired, Mr. Morgenthau reached a $536 million settlement with Credit Suisse, Switzerland’s second-largest bank, which had helped Iranian, Libyan and Sudanese clients hide shady business in America.

But Mr. Morgenthau spent years working with federal prosecutors investigating the Bank of Credit and Commerce International, a global enterprise founded by Middle Eastern investors as a nexus for money that flowed in and out of drug cartels, terrorist groups and dictatorships. In 1991, the bank pleaded guilty to federal and state charges in what Mr. Morgenthau called the largest bank fraud in financial history, with losses estimated at $15 billion. It was forced to close, pay fines and forfeit all its assets.

He also indicted Clark M. Clifford, an adviser to Democratic presidents, and his law partner Robert A. Altman on charges of taking $40 million in bribes for helping the bank gain control of a large bank holding company. Mr. Clifford’s failing health led to the dismissal of charges against him, and Mr. Altman was acquitted.

The Target of Protests

Although he cultivated an image of imperviousness to public pressure, Mr. Morgenthau was often barraged with criticism, particularly in cases involving racial bias or police brutality. Critics said he was slow to respond to an epidemic of police corruption in the 1980s, including cases in which transit officers falsely arrested eight black men, who sued and collectively won $1 million in damages.

After the 1983 death in custody of Michael Stewart, a 25-year-old black graffiti artist arrested for spray-painting on a subway station wall, six white transit officers who had handcuffed him and were seen forcing a nightstick down on his neck were acquitted of criminal charges in 1985. The verdicts touched off protests by people who contended that Mr. Morgenthau had mishandled the prosecution.

And in a case that seemed to confirm national impressions of New York City as a cesspool of crime and race hatred, Mr. Morgenthau was vilified for what many called a waffling prosecution of Mr. Goetz, a white loner who shot four young black men on a subway train in 1984 after they surrounded him and demanded money. One victim was left paralyzed and partly brain-damaged.

“You don’t look so bad, here’s another,” the gunman told one prone victim as he fired again and fled.

Variously hailed as a hero who acted in self-defense and denounced as a racist self-appointed vigilante, Mr. Goetz was first indicted only for illegal possession of a gun. After a public outcry, another grand jury indicted him for attempted murder. But the more serious charges were dismissed on a technicality, and he was finally convicted in 1987 on a weapons charge and served six months in jail.

The disappearance of a 6-year-old boy, Etan Patz, from a Manhattan street in 1979 — a case that generated a movement to raise public awareness, increase law-enforcement resources and pass new legislation to find missing children — riveted the city and the nation for decades, as theories and suspects came and went without sufficient evidence for a prosecution during Mr. Morgenthau’s tenure.

But the case was reopened by District Attorney Cyrus R. Vance Jr. in 2012, and Pedro Hernandez, a former bodega stock clerk who confessed to luring Etan into a basement and attacking him, was found guilty in 2017 of kidnapping and murdering the boy. Mr. Hernandez, 56, who had lived in New Jersey for years, was traced through a tip from his brother-in-law. He was sentenced to 25 years to life in prison.

Mr. Morgenthau lost about a quarter of his cases, and some that he won proved to be miscarriages of justice. The most glaring example was the conviction of five young black and Latino men from Harlem, four of whom falsely confessed on videotape to the 1989 beating and rape of the 28-year-old investment banker who became known as the Central Park Jogger.

After serving terms of 7½ to 13 years, the five were exonerated in 2002 after an imprisoned serial rapist and murderer, Matias Reyes, confessed to the crime. Mr. Morgenthau ordered a new investigation, including DNA tests that confirmed the Reyes account, and moved to clear the men in court.

“If only we had DNA 13 years ago,” Mr. Morgenthau lamented.

“I think it was his finest hour,” said Barry Scheck, a founding director of the Innocence Project of the Benjamin N. Cardozo School of Law, which promotes the use of DNA to reverse wrongful convictions. “Very few D.A.s would have done that, but he could with his stature, self-confidence, guts and commitment to principle. In that and other cases I’ve seen, I believe he has asked, ‘Is this the right thing to do?’ ”

A Revered Institution

Mr. Morgenthau was probably the most innovative prosecutor in the city’s history. To pursue financial crimes, he hired scores of accountants and detectives with financial expertise. He promoted DNA testing and other modern investigating techniques. Enlarging the homicide bureau and other units, he hired Spanish-speaking interpreters and hundreds of black, Hispanic and female prosecutors, and he created the office’s first sex-crimes and consumer affairs units.

He stressed the prosecution of career criminals, drug pushers, child pornographers, landlords who harassed tenants and perpetrators of attacks on gay men and lesbians. And throughout his tenure he opposed the death penalty, arguing that it was inhumane and was ineffective as a deterrent.

In later years, many New Yorkers wondered if he was too old for the job. As he ran for a ninth term in 2005, he faced rigorous opposition in a Democratic primary for the first time in decades. The challenger, Leslie Crocker Snyder, a former state court judge, was endorsed by a number of longtime Morgenthau supporters. But Mr. Morgenthau won the primary, 59 to 41 percent, and the general election, with 99 percent of the vote. He had run unopposed in general elections for 20 years, and did so again in this, his last race.

In a grandfatherly cardigan, his lanky legs propped on a desk and his wispy white hair afloat, Mr. Morgenthau looked like an aging prep-school master, not America’s best-known D.A., a model for the prosecutor played by Steven Hill on the long-running TV drama “Law & Order.” Some took his occasionally mismatched socks for absent-mindedness and his guttural voice for gruffness. He was typically mild-mannered.

Despite his highbrow upbringing, his inflections were New York: “had to” came out “hadda.” He loved Dunhill Montecruz cigars, allowing himself two a day until he quit years ago. His health seemed good even in his later years. But decades of strain in one of the city’s most demanding jobs were apparent in the stooped shoulders and the gaunt face lined with legal decisions.

By 2009, when he decided not to run for another term, Mr. Morgenthau was a virtual institution, despised by the enemies a prosecutor inevitably acquires but widely admired by New Yorkers and revered by generations of assistants he had hired and mentored, many of whom had gone on to judgeships and careers in politics and the law — extensions of his influence who regarded him as an embodiment of integrity.

His former protégés included Associate Justice Sonia Sotomayor of the United States Supreme Court; Gov. Andrew M. Cuomo; former Gov. Eliot Spitzer; Lanny A. Breuer, head of the Justice Department’s criminal division; and Cyrus R. Vance Jr., who succeeded him as the district attorney.

Looking back on Mr. Morgenthau’s career, Mitchell L. Moss, a professor of urban policy at New York University, said in 2011, “He turned the district attorney’s office into the premier law-enforcement office in the country, apart from the United States attorney general’s office.”

From War to Law

Robert Morris Morgenthau was born in Manhattan on July 31, 1919. His grandfather, the real estate tycoon Henry Morgenthau Sr., was President Wilson’s ambassador to the Ottoman Empire in World War I and a prominent voice against Armenian genocide. Robert’s father, Henry Jr., was Roosevelt’s treasury secretary from 1934 to 1945, and his mother, Elinor (Fatman) Morgenthau, was a niece of Herbert H. Lehman, the New York Democratic governor and United States senator.

Robert grew up with his brother, Henry III, and his sister, Joan, in New York City, on the family’s farm in upstate East Fishkill, N.Y., and in a privileged world of estates, private schools and social connections, notably with the Kennedys of Boston and Hyannis Port, Mass., and the Roosevelts of Hyde Park, N.Y. He attended the Lincoln School in Manhattan and graduated from the Deerfield Academy in Massachusetts in 1937 and from Amherst College in 1941 with high honors and a political science degree.

As a young man, he raced sailboats with Jack Kennedy off Cape Cod, spent memorable New Year’s Eves at the White House with his father, and in 1939 roasted hot dogs for King George VI and Queen Elizabeth of Britain at the home of his Hudson Valley friends Franklin and Eleanor Roosevelt. (On leave from the Navy during World War II, he served mint juleps to Winston Churchill and F.D.R. on the lawn of his family’s apple farm.)

While studying at Amherst, Mr. Morgenthau met Martha Pattridge, a Smith College student. They were married in 1943 and had five children. His first wife died in 1972. In 1977 he married Ms. Franks, a Pulitzer Prize-winning journalist. They had two children.

Besides his wife, he is survived by the children of his first marriage, Jenny Morgenthau, Anne Morgenthau Grand, Elinor Morgenthau, Robert P. Morgenthau and Barbara Morgenthau Lee; the children of his second marriage, Joshua Franks Morgenthau and Amy Elinor Morgenthau; and by six grandchildren and three great-grandchildren.

In 2014, Ms. Franks published a memoir, “Timeless: Love, Morgenthau, and Me,” that focused on her long and passionate union with a man almost 30 years her senior.

Mr. Morgenthau had been in the Naval Reserve in college, and after graduation he went on active duty as an ensign. He passed his physical exam by concealing the near-deafness in his right ear from a boyhood mastoid infection. An officer aboard three destroyers and a minesweeper during World War II, he survived enemy attacks and won decorations for bravery under fire.

His destroyer, the U.S.S. Lansdale, was attacked by Nazi torpedo bombers in the Mediterranean off Algiers on April 20, 1944. Cut by explosions, the ship went down with a heavy loss of life. Lieutenant Morgenthau, the executive officer, saved several shipmates, leapt into the water and swam for three hours in the darkness until he and others were picked up by an American warship. In 1945 his ship, the U.S.S. Harry F. Bauer, was hit by a Japanese kamikaze plane off Iwo Jima, but its 550-pound bomb did not explode.

Mustering out after the war as a lieutenant commander, he enrolled in Yale Law School, finished a three-year course in two years and graduated in 1948. He soon joined the New York law firm Patterson, Belknap & Webb and became the personal assistant to the senior partner, Robert P. Patterson, who had been President Harry S. Truman’s secretary of war.

Besides practicing corporate law, Mr. Patterson defended people swept up in the anti-Communist witch hunts of the 1950s, including the actor Edward G. Robinson, who testified before the House Un-American Activities Committee and resisted blacklisting. “Unlike most Wall Street lawyers of that day, he would take loyalty cases,” Mr. Morgenthau said of Mr. Patterson, one of his early heroes. “He didn’t care what anybody else thought. He did what he thought was right.”

Mr. Patterson died in a plane crash in 1952. Mr. Morgenthau was supposed to have been on the flight — he had accompanied his boss on every other trip — but stayed behind to write a brief. Mr. Morgenthau was a partner in the firm from 1954 to 1961.

On the Kennedy Bandwagon

After practicing law for 12 years, Mr. Morgenthau, who had dabbled in Democratic politics in the Riverdale section of the Bronx, where he lived, jumped on the Kennedy bandwagon in 1960 and became chairman of Bronx Citizens for Kennedy. His reward was appointment in 1961 as the United States attorney for the Southern District of New York, embracing Manhattan, the Bronx and six upstate counties.

His most notable early case was the 1962 conviction of State Supreme Court Justice J. Vincent Keogh and Anthony (Tony Ducks) Corallo, a mobster who got his nickname ducking subpoenas and convictions, on charges of attempted bribery to influence a federal bankruptcy fraud case.

But after 17 months in office, Mr. Morgenthau left at the urging of the president’s brother, Attorney General Robert F. Kennedy, for a quixotic 1962 run to unseat Gov. Nelson A. Rockefeller, a rising star in the Republican Party’s moderate wing. It was a fiasco. Distant and seemingly distracted at campaign stops, from which he sometimes wandered away, Mr. Morgenthau lost by 500,000 votes.

After the election, President Kennedy reappointed him to the federal prosecutor’s job, and he waded in zealously. He created the office’s first special unit to investigate Wall Street and over the next seven years brought charges against stock manipulators, money launderers, tax lawyers and Internal Revenue Service accountants. He also indicted 150 organized crime figures.

Always close to the Kennedys, Mr. Morgenthau was with Robert Kennedy at his home in McLean, Va., on Nov. 22, 1963, when the F.B.I. director J. Edgar Hoover called to report that the president had been shot in Dallas. Years later, facing criticism for hiring John F. Kennedy Jr. as an assistant district attorney, he snapped, “If having a famous father were a disqualification, I wouldn’t have gotten my job.”

He had overwhelming conviction rates but lost two cases against Roy M. Cohn, the aggressive former counsel to the anti-Communist crusader Senator Joseph R. McCarthy. Acquitted in 1964 of perjury in a stock swindle and in 1967 of mail fraud in a bus-line takeover, Mr. Cohn accused the prosecutor of waging a vendetta against him.

“A man is not immune from prosecution just because a United States attorney happens not to like him,” Mr. Morgenthau remarked.

In 1968 he again convicted Mr. Corallo, this time for bribing James L. Marcus, a former city water commissioner, to win contracts for renovating the Jerome Park Reservoir in the Bronx. In 1969 Carmine De Sapio, the last Tammany Hall power broker, whose prescription dark glasses gave him a sinister air, was also convicted of conspiring to bribe Mr. Marcus, who went to prison for taking kickbacks.

A City in Disarray

After resisting pressure from the Nixon administration for a year, Mr. Morgenthau resigned as federal prosecutor in January 1970. He was briefly a deputy to Mayor John V. Lindsay, but quit to again run for governor. Short of funds and support, he soon withdrew from the Democratic primary. Governor Rockefeller defeated the Democratic candidate, Arthur J. Goldberg, in the general election.

Mr. Morgenthau practiced law privately until 1974. He then jumped into a special election necessitated by the resignation (and impending death) of Mr. Hogan, Manhattan’s district attorney for 32 years, and easily defeated the interim appointee, Richard H. Kuh.

When he took office in 1975, the city was in trouble, threatened by bankruptcy, public-employee strikes and a fraying social fabric. Buildings were abandoned and burned. Garbage piled up in the streets. Graffiti covered subways and buses. Crime was rampant, with 648 murders in Manhattan alone that year. (There were 58 the year he left office.)

The prosecutor’s office was in disarray, too. Many of its 195 lawyers had no phones. Its $8 million budget ran out halfway through the fiscal year. There was little expertise for combating sophisticated criminality. Case processing was inefficient, with different lawyers handling arraignments, indictments and trials.

Mr. Morgenthau streamlined the system, achieving greater speed and higher conviction rates by having one lawyer see each case through to completion. His growing influence helped win new laws mandating forfeiture of gains from criminal activity and limiting jury trials for misdemeanors.

His victories included the 1981 convictions of Mr. Chapman in the killing of John Lennon, and of a Metropolitan Opera stagehand, Craig Crimmins, in the murder of a violinist at Lincoln Center; the 1988 manslaughter guilty plea of Mr. Chambers in the strangulation of Jennifer Levin in Central Park; the 1989 manslaughter conviction of Joel Steinberg in the beating death of his adopted daughter, Lisa; and the convictions in 1991 and 1992 of seven men in the subway murder of a Utah tourist, Brian Watkins.

At the end of his last term, Mr. Morgenthau was 90 and had served three years longer than Mr. Hogan. He joined the Manhattan law firm Wachtell, Lipton, Rosen & Katz. Besides pro bono work, he wrote numerous op-ed articles in The Wall Street Journal, The Daily News and The New York Times calling for immigration reform, crackdowns on illegal guns, and improved care for veterans of the Iraq and Afghanistan wars suffering from post-traumatic stress disorders.

In an interview with The New York Times in 2009 after announcing that he would not seek a 10th term, Mr. Morgenthau ruminated on the night in 1944 when his ship was torpedoed by Nazi warplanes and went down with 47 of his shipmates.

“I was swimming around without a life jacket,” he recalled. “I made a number of promises to the Almighty, at a time when I didn’t have much bargaining power.”

His deal?

“That I would try to do something useful with my life.”

Dennis Hevesi, a former New York Times reporter who died in 2017, and Kaly Soto contributed reporting.

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