The Morgan Freeman-narrated "March of the Penguins" was named best documentary and Hany Abu-Assad's "Paradise Now" was hailed as the best foreign film, Daily Variety said.
Clooney lost to Ang Lee in the director's category, who won the honor for "Brokeback Mountain.
The National Board of Review's top actor was Philip Seymour Hoffman for "Capote" and Felicity Huffman won best actress for "Transamerica."
Stephen Gaghan won best adapted screenplay honors for "Syriana" and Noah Baumbach won the best original screenplay award for "The Squid and the Whale."
"Tim Burton's Corpse Bride" was named top animated feature and "King Kong" was hailed for special effects.
The awards will be handed out at New York's Tavern on the Green Jan. 10.