The nominations were announced Thursday morning in Manhattan.
Prizes will be presented by the Independent Filmmaker Project, a U.S. advocacy organization for independent filmmakers, at a ceremony Dec. 2 at Cipriani Wall Street.
The nominees for Best Feature are "12 Years a Slave," "Ain't Them Bodies Saints," "Before Midnight," "Inside Llewyn Davis" and "Upstream Color."
Shortlisted for Best Documentary are "The Act of Killing," "The Crash Reel," "First Cousin Once Removed," "Let the Fire Burn" and "Our Nixon."
In the running for the Bingham Ray Breakthrough Director Award are Ryan Coogler for "Fruitvale Station," Adam Leon for "Gimme the Loot," Alexandre Moors for "Blue Caprice," Stacie Passon for "Concussion" and Amy Seimetz for "Sun Don't Shine."
Vying for the Best Actor title are Chiwetel Ejiofor for "12 Years a Slave," Oscar Isaac for "Inside Llewyn Davis," Matthew McConaughey for "Dallas Buyers Club," Robert Redford for "All Is Lost" and Isaiah Washington for "Blue Caprice."
Nominated for Best Actress are Cate Blanchett for "Blue Jasmine," Scarlett Johansson for "Don Jon," Brie Larson for "Short Term 12," Amy Seimetz for "Upstream Color" and Shailene Woodley for "The Spectacular Now."
The nominees for the Breakthrough Actor trophy are Dane DeHaan for "Kill Your Darlings," Kathryn Hahn for "Afternoon Delight," Michael B. Jordan for "Fruitvale Station," Lupita Nyong'o for "12 Years a Slave" and Robin Weigert for "Concussion."
"The Gotham Awards celebrate and showcase the very best of the vibrant, entertaining, challenging, and innovative films presented by our community, and help new audiences discover this vital work. We congratulate this year's master film artists, talented newcomers, and other nominees representing the rich and diverse spectrum of today's independent filmmaking," Joana Vicente, executive director of IFP and the Made in NY Media Center, said in a statement. "We also want to thank our nominating committees of film critics, journalists, programmers and film curators for their dedication to selecting the nominees from so many worthy submissions."