Both contenders were nominated for best picture by the Independent Film Project in the East Coast equivalent of the Indie Spirit Awards.
Also in the running are "A History of Violence" and two lower-budget indies, "Keane" and "You and Me and Everyone We Know."
"Brokeback Mountain," starring Heath Ledger and Jake Gyllenhaal as ill-fated lovers, also received a nomination for best ensemble cast, as did "Crash," "Good Night, and Good Luck," "The Squid and the Whale" and "Nine Lives."
Bennett Miller received a nod as breakthrough director for "Capote" starring Philip Seymour Hoffman as the writer, along with Miranda July ("Me and You and Everyone We Know"), Phil Morrison ("Junebug"), Andrew Wagner ("The Talent Given Us") and Alice Wu ("Saving Face").
Nominations for breakthrough actor went to Amy Adams ("Junebug"), Camilla Beale ("The Ballad of Jack and Rose"), Joseph Gordon-Levitt ("Mysterious Skin"), Terrence Howard ("Hustle & Flow") and Damian Lewis ("Keane").
Best documentary noms went to "Ballets Russes," "Enron: The Smartest Guys in the Room," "Grizzly Man," "Murderball" and "William Eggleston in the Real World."
Nominations were also announced yesterday for the British Independent Film Awards which, like the Gothams, will be given out Nov. 30.
The musical dramedy "Mrs. Henderson Presents" and the period drama "The Libertine" led with eight nominations apiece. Fernando Mereilles' drama "The Constant Gardener" received seven.