In the film, director Dror Moreh explores intelligence operations by Israel's Shin Bet security agency.
The prize for best picture went to "Amour," whose star Emmanuelle Riva was chosen as the best actress.
Daniel Day-Lewis was chosen best actor for "Lincoln."
The group of 60 prominent movie critics from around the country met at Lincoln Center in New York City to make its picks.
Austrian director Michael Haneke won best director for "Amour." The French-language movie depicts the slow deterioration of the elderly woman played by Riva. It has been praised as an unflinching look at old age and life's end.
Playwright Tony Kushner won best screenplay for "Lincoln."
Amy Adams was chosen best supporting actress for "The Master," and Matthew McConaughey was selected best supporting actor for "Magic Mike" and "Bernie."
Mihai Malaimaire was honored for best cinematography for "The Master."
The film critics' society, founded in 1966, works to promote film preservation and historically important movies.
This year's awards were dedicated to the late Village Voice critic Andrew Sarris, a founding member of the society, who died last year.