"The Tree of Life," starring Brad Pitt and Sean Penn, and the comedy "Beginners," starring Ewan McGregor, tied for Best Feature.
Natalie Portman, who was a jury member, said they couldn't decide which film was better.
One of this year's Gotham Tributes went to actress Charlize Theron.
"The career that I've been able to have, the people that I've been able to work with, the fact that I never had to get a second job to pay the bills - that was really the reward," said Theron.
Other Gotham Tributes went to director David Cronenberg, film executive Tom Rothman and actor Gary Oldman.