The film, which recounts the story of one of the planes hijacked during the terrorist attacks of September 11, 2001, topped the list, above the film The Queen.
Helen Mirren, the actress who played Elizabeth II in The Queen, was named best actress, and the project also won the prize for best screenplay.
Forest Whitaker took the best actor award for his role in the film The Last King of Scotland.
Martin Scorsese was named best director for his film The Departed.
The president of the critics group said of United 93, "I think everybody agrees it was an amazing film in terms of telling the story without pushing a political point of view."