I thought Pesci deserved it specifically because he didn't dominate the film. It was the complete opposite of his performances in Goodfellas or Casino, loud and brash and in your face. He did a superb job reminding everyone who remembers him post-retirement for Goodfellas and Home Alone that he has much more range than just "short angry asshole".
He was great in the movie. De Niro was too. Pacino was even better than both of them, granted he had the flashiest role. Really great acting all around. My only gripe is that Harvey Keitel didnt have a larger role.