The best picture winner also garnered best director awards for Richard Linklater and best supporting actress for Patricia Arquette.
It was shot over more than a decade to capture the passage of time in one boy's life from age 5 to 18.
The annual critics awards are typically viewed as a pre-cursor to the high-profile and coveted Academy Awards.
Other winners include actor Timothy Spall - named best actor for British painter JMW Turner in Mr Turner - and best actress Marion Cotillard for her roles in The Immigrant and Two Days, One Night.
Actor JK Simmons won a best supporting actor prize for his role as a terrorising music teacher in Whiplash.
The Lego Movie won best animated film, while Ida was named best foreign film. Citizenfour, about US intelligence whistleblower Edward Snowden, won for best documentary film.
Presentation of the awards is scheduled for 5 January in New York.
The New York Film Critics Circle, founded in 1935, counts members representing magazines, newspapers and online publications.
The awards are considered a bellwether for the Oscars, which will air on 22 February.
Boyhood, a film 12 years in the making, has won top honours at the New York Film Critics awards.