Bigelow also won best director for the picture, her first film since the 2009 Iraq war drama, "The Hurt Locker," while Greig Fraser won for cinematography, reported Los Angeles Times.
Both "The Hurt Locker" and Bigelow took top honors from the organization three years ago.
"Zero Dark Thirty" is set to open in theaters on December 19.
Daniel Day-Lewis was named best actor for his portrayal of Abraham Lincoln in Steven Spielberg's epic "Lincoln," and Sally Field was named best supporting actress as the 16th's president's wife, Mary Todd Lincoln.
The "Lincoln" win marks Day-Lewis' fifth award from the critics organization. The last time he won was five years ago for "There Will Be Blood." Field won best actress from the NYFCC 33 years ago for "Norma Rae."
Tony Kushner also won for his screenplay for "Lincoln."
Rachel Weisz won best actress for "The Deep Blue Sea," as a married woman who has an affair with a dashing RAF pilot.
Supporting actor honors went to Matthew McConaughey for his roles as a local district attorney in "Bernie" and as the owner of a male strip club in "Magic Mike."
"Amour," director Michael Hanke's drama about an elderly couple, was named best foreign film.
The best animated film honour went to Tim Burton's "Frankenweenie."
The film also recently earned an Annie Award nomination for best animated feature.
The New York Film Critics Circle, which was founded in 1935, is made up of critics from daily and weekly newspapers, magazines and qualifying online sites.