The film received four nominations in the Gothams' six categories, including Best Feature, Best Actor for Ethan Hawke, Best Actress for Patricia Arquette and Breakthrough Actor for Ellar Coltrane.
Alejandro G. Inarritu's "Birdman," Justin Simien's "Dear White People," Dan Gilroy's "Nightcrawler" and Jonathan Glazer's "Under the Skin" received two nominations each.
"Boyhood," "Birdman" and "Under the Skin" will compete in the Best Feature category against "The Grand Budapest Hotel" and "Love Is Strange," while the Best Documentary category consists of "Actress," "CitizenFour," "Life Itself," "Manakamana" and "Point and Shoot."
Acting nominations went to a few contenders who are also in the running for Oscars, including Arquette, Hawke, Michael Keaton for "Birdman" and Julianne Moore for "Still Alice," as well as a number of dark horses: Miles Teller for "Whiplash," Bill Hader for "The Skeleton Twins," Scarlett Johansson for "Under the Skin" and Gugu Mbatha-Raw for "Beyond the Lights."
Each category was selected by a separate jury consisting in most cases of film critics, which led to some disconnects: While Steve Carell, Channing Tatum and Mark Ruffalo were voted a special group acting award for "Foxcatcher," for instance, that film was shut out of all other categories, including Best Feature.
The director of "Foxcatcher," Bennett Miller, is being honored with a special tribute at this year's Gothams ceremony.
"Whiplash" and "A Most Violent Year" also showed up in acting categories but nowhere else.
The New York-based Gotham Awards are one of the two major honors for independent film, and will be presented early in awards season, on Dec. 1 at Cipriani Wall Street.
The other major indie awards show, the Film Independent Spirit Awards, takes place in Los Angeles at the end of the season, the day before the Oscars.
"Point and Shoot"
Bingham Ray Breakthrough Director Award
Ana Lily Amirpour for "A Girl Walks Home Alone at Night)"
James Ward Byrkit for "Coherence"
Dan Gilroy for "Nightcrawler"
Eliza Hittman for "It Felt Like Love"
Justin Simien for "Dear White People"
Bill Hader in "The Skeleton Twins"
Ethan Hawke in "Boyhood"
Oscar Isaac in "A Most Violent Year"
Michael Keaton in "Birdman or (The Unexpected Virtue of Ignorance)"
Miles Teller in "Whiplash"
* The 2014 Best Actor nominating panel also voted to award a special Gotham Jury Award jointly to Steve Carell, Mark Ruffalo and Channing Tatum for their ensemble performance in "Foxcatcher."
Patricia Arquette in "Boyhood"
Gugu Mbatha-Raw in "Beyond the Lights"
Julianne Moore in "Still Alice"
Scarlett Johansson in "Under the Skin"
Mia Wasikowska in "Tracks"
Riz Ahmed in "Nightcrawler"
Macon Blair in "Blue Ruin"
Ellar Coltrane in "Boyhood"
Joey King in "Wish I Was Here"
Jenny Slate in "Obvious Child"
Tessa Thompson in "Dear White People"
Spotlight on Women Filmmakers 'Live the Dream' Grant
Garrett Bradley, director, "Below Dreams"
Claire Carré, director, "Embers"
Chloé Zhao, director, "Songs My Brothers Taught Me"