After decades in prison, three men were cleared Friday in one of the most horrifying crimes of New York’s violent 1990s — the killing of a clerk who was set on fire in a subway toll booth.

A judge dismissed the murder convictions of Vincent Ellerbe, James Irons and Thomas Malik after Brooklyn District Attorney Eric Gonzalez cited “serious problems with the evidence on which these convictions are based.” He pointed to doubts about the men’s confessions and problems with witness identifications.

The three confessed to and were convicted of murdering token seller Harry Kaufman in 1995. The case resounded from New York to Washington to Hollywood, after parallels were drawn between the deadly arson and a scene in the movie “Money Train.”

“The findings of an exhaustive, years-long reinvestigation of this case leave us unable to stand by the convictions,” Brooklyn District Attorney Eric Gonzalez said in a release. He cited “serious problems with the evidence on which these convictions are based” and acknowledged “the harm done to these men by this failure of our system.”

The confessions conflicted with evidence at the scene and with each other, and witness identifications were problematic, prosecutors say. Some of the men have long said they were coerced into falsely confessing in the case, which had a lead detective who later was repeatedly accused of forcing confessions and framing suspects.

Ellerbe, 44, was paroled in 2020, but Malik and Irons, both 45, had remained in prison until Friday. Irons wiped away tears during much of the court proceeding.

"It's a nightmare. You don't know what it's like to really be inside that cell," Ellerbe told reporters.

"They knew the truth all along, but they withheld it, deliberately, intentionally," Malik said, believing police and prosecutors were responsible for the trio's imprisonment.

Malik was still getting his head around the long-awaited news Friday morning that prosecutors were reconsidering the case, lawyer Ronald Kuby said.

“Yesterday was the first day that he actually allowed himself to believe that he’s going to be free,” said Kuby, who also represents Ellerbe and said the latter is “extraordinarily happy” to see his conviction thrown out.

Kaufman was working an overnight shift at a Brooklyn subway station on Nov. 26, 1995, when attackers first tried to rob him, then squirted gasoline into the booth and ignited it with matches while he pleaded, “Don’t light it!,” authorities said at the time. The booth exploded, and the 50-year-old Kaufman ran from it in flames. The married father died two weeks later.

The attack bore some resemblance to a scene in “Money Train,” an action movie that had been released four days earlier. Then-Senate Majority Leader and Republican presidential hopeful Bob Dole took to the Senate floor to call for a boycott of the movie.

Authorities gave mixed signals over the years about whether they believed the film had inspired the killing.

Police scoured for suspects and eventually came to question Irons, getting a confession that he was acting as a lookout. He implicated Malik and Ellerbe as the men who had torched the tollbooth.

From their arrests on, Ellerbe and Malik maintained that they had been coerced into false confessions, with Malik saying that Detective Louis Scarcella had screamed at him and slammed his head into a locker. Scarcella testified that he cursed, pounded a table and was trying to scare the then 18-year-old Malik but didn’t beat him.

Gonzalez’s office said its review found that Scarcella and his partner fed important details about the crime scene to Irons — details that prosecutors later used at trial to argue that his confession was so specific that it had to be true. But it included clearly dubious claims. For instance, he said, he had been able to see his supposed accomplices jump into a getaway car, though it was parked a block away and around a corner, prosecutors said.

At the time, Scarcella was a star Brooklyn homicide detective in a city reeling from crime. Citywide, killings topped more than 2,200 at their 1990 peak; that compares to 488 last year and a low of 295 in 2018.

But after questions accumulated about Scarcella’s tactics, the Brooklyn district attorney’s office began in 2013 to review scores of cases that he had worked.

Scarcella, who retired in 2000, has denied any wrongdoing. While more than a dozen convictions in his cases have been overturned, prosecutors have stood by scores of others.

Brooklyn prosecutors’ reexamination of old convictions is widely viewed as one of the most ambitious of its kind. In New York and around the country, such efforts have become more common over the last 15 years as DNA evidence, a growing body of research on false confessions, and other factors made some prosecutors feel compelled to become more open to investigating wrongful conviction claims.

“This is no longer about one or two bad apples,” Kuby said. “This is about a systemic rot.”