The film won over Richard Linklater's "Boyhood," which was chosen for the audience award and hailed best picture by the New York Film Critics Circle.
"I did this film for all of us that in our age are still wandering and questioning what...life is about, what's the point of all of this," the film's director Alejandro Gonzalez Inarritu said in his acceptance speech.
Michael Keaton won best actor for portraying the film's lead, Variety reports.
"I want to thank the folks of Gotham," Keaton said in his acceptance speech, joking about "Batman." "It's good to be home."
Uma Thurman hosted the show and Scarlett Johansson, Meryl Streep and John Hamm were among the many award presenters, says Time.
The 2014 Gotham Awards was also a big night for Julianne Moore who took home the best actress trophy for "Still Alice." "Citizenfour," a film about Edward Snowden, directed by Laura Poitras was chosen as best documentary.
Ana Lily Amirpour took home the Binham Ray Breakthrough Director Award for her work on "A Girl Walks Home Alone At Night."
Tessa Thompson won the award for Breakthrough Actor for her role in "Dear White People." Accepting the award, Thompson said: "I didn't expect for this to happen, so I made jokes about losing all week. Thanks to filmmakers who take risks. Those are the ones that make me excited about doing what I do."
"Foxcatcher," which starred comedian Steve Carell among others, won best ensemble. Bennett Miller, who was also part of "Foxcatcher" won the career tribute award in directing.
Netflix's Ted Sarandos also received a career tribute award. And Tilda Swinton was the third recipient of the career tribute trophy.
The 2014 Gotham Awards was hosted by the Independent Film Project.
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