The two movies will face stiff competition from thriller The Loneliest Planet, drama Middle of Nowhere and director Richard Linklater's black comedy Bernie, which has also scored a nomination for Best Ensemble Performance.
The casts of Moonrise Kingdom, Safety Not Guaranteed, Your Sister's Sister and Bradley Cooper and Robert De Niro's Silver Linings Playbook are also up for the top prize, although The Master, starring Joaquin Phoenix and Philip Seymour Hoffman, is a surprise omission.
Quvenzhane Wallis' performance in Beasts of the Southern Wild has earned the child star a nod in the Breakthrough Actor category, where she'll be up against Mike Birbiglia (Sleepwalk with Me), Emayatzy Corinealdi (Middle of Nowhere), Thure Lindhardt (Keep the Lights On) and Melanie Lynskey (Hello, I Must Be Going), while her director Benh Zeitlin will face off against the likes of Zal Batmanglij (Sound of My Voice), Jason Cortlund and Julia Halperin (Now, Forager) for the Breakthrough Director honour.
Detropia, How to Survive a Plague, The Waiting Room and Room 237 are among the nominees for Best Documentary.
Meanwhile, Matt Damon, French actress Marion Cotillard and filmmaker David O'Russell will receive career tributes at the New York ceremony, which will take place on 26 November (12).
The Big Apple prizegiving traditionally kicks off the film world's awards season with winners often going on to land Academy Awards nominations and wins.