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Muhammad Aziz, 84, is seeking $40 million (£34m) for the two decades he spent in prison and more than 55 years of being wrongly blamed for the murder of the civil rights leader in 1965.
He said the wrongful conviction caused "immense and irreparable" damage to him and his family.
Mr Aziz, Khalil Islam and a third accused Mujahid Abdul Halim were convicted in March 1966 for shooting dead the Nation of Islam spokesperson and civil rights activist the year before in Harlem. Islam died in 2009.
A similar $40 million lawsuit has been filed in Brooklyn federal court by the estate of Islam who was exonerated after spending 22 years in prison.
"They got a small measure of justice when their convictions were vacated," Deborah Francois, a lawyer for both plaintiffs, said in an interview on Thursday.
"But we want to hold government officials accountable for misconduct that led to their wrongful convictions and decades of living with the stigma of being labeled Malcolm X’s murderers."
Settlement talks had proven unsuccessful.
Mayor Eric Adams, a former police captain, said the city was reviewing the lawsuits and called overturning both convictions "the just outcome."
Malcolm X was the leading figurehead of the Nation of Islam but left the Black seperatist group in 1964.
The civil rights advocate was shot dead at age 39 in February 1965 while preparing to speak at New York’s Audubon Ballroom.
A third man, Mujahid Halim, was also convicted for the shooting.
He testified that Aziz and Islam were innocent.
Halim was paroled in 2010.
In recommending that Aziz’s and Islam’s convictions be dismissed, then-Manhattan District Attorney Cyrus Vance cited new evidence that authorities withheld "dozens and dozens" of documents from the defense including exculpatory evidence.
Last year, members of Malcolm X’s family made public what they described as a letter written by a deceased police officer stating that the New York Police Department and FBI were behind the 1965 killing of the famed Black activist and civil rights advocate.
At the time, the NYPD said it was reviewing the matter and the FBI declined to comment.