This movie is 20? Years old. About a boy who as a prank pushes a wheel chair down subway steps and hurts someone. Takes place in New York. He's sent to a reform school? Where he and others there are raped by priests? At the school. Later, as an adult, he takes
Vengeance by finding the man who raped him and shooting him. This movie was
Condemned by the Church who said it wasn't true.

You may be thinking of the movie "Sleepers" with Kevin Bacon, Robert De Niro, Brad Pitt, and Billy Crudup:

http://en.wikipedia.org/wiki/Sleepers_(film)