Technically yes. But you probably won't be able to recognize him.
On the director's commentary of the Malcolm X DVD, Spike Lee says that while he wanted to include some kind of footage of JFK's assassination in Malcolm X, Lee's film schedule was already running long and expensive. Spike knew Oliver Stone and that he had been shooting J.F.K. at about the same time and simply asked Oliver for footage to use in Malcolm X (both films are Warner Brothers films so negotiating all of the rights & permissions to do this was not utterly impossible). Lee used footage Stone passed on in Malcolm X.
The footage Spike Lee uses is all predominantly long shots and so it is hard to see individual actors, but the actors playing JFK, Jackie, Governor & Mrs Connally, a Limo Driver, a Secret Service Man, and Bill Newman (a witness to the JFK assassination played by @vincentdonofrio) are all credited in the Malcolm X press kit (in a section marked 'JFK Sequence')
I count this technically as an appearance for Vincent D'Onofrio because he's credited in the press materials and in the film's end credits but he might not and fans of his work could also argue that since there isn't much to see, it's not really one of Vincent D'Onofrio films.