The movie about the hunt for terror leader Osama bin Ladin also earned Bigelow the Best Director honor and writer Mark Boal the award for Best Screenplay.
Daniel Day-Lewis was named Best Actor for his work in "Lincoln."
Emmanuelle Riva took the prize for Best Actress for "Amour," which also received NYFCO's award for Best Foreign Language film.
The stars of actor-director Ben Affleck's "Argo" were declared Best Ensemble Cast.
Benh Zeitlin's "Beasts of the Southern Wild" was feted for Best Breakthrough Performance by Quvenzhane Wallis, while Zeitlin was honored as Best Debut Director.
The Spanish-language "Chico & Rita" was honored as Best Animated Feature, while "The Central Park Five" was selected as Best Documentary.
"Life of Pi" won for Best Cinematography.
NYFCO's Top 10 in alphabetical order are "Argo," "Beasts of the Southern Wild," "Django Unchained," "Les Miserables," "Life of Pi," "Lincoln," "The Master," "Moonrise Kingdom," "Silver Linings Playbook" and "Zero Dark Thirty."