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.

HP split into two separate companies in November - one focused on the printer and PC businesses and the other on corporate services.
Shares of Hewlett Packard Inc fell 4% while services focussed Hewlett Packard Enterprises rose 2.3%.
The Dow Jones gained 19 points to close at 17,812, after a bumpy start.
The S&P 500 rose 2 points to 2,079.22, while the Nasdaq gained 20 points to 5,102.
Hewlett-Packard's revenue fell 9.5% to $25.71bn in the fourth-quarter.
On a broader theme, concerns about global political tensions weighed on early trading after it was reported that Turkey had shot down a Russian warplane.
Stocks regained their footing, though on the back of news that the US economy grew faster than previously estimated in the third quarter of the year.
The Commerce Department said gross domestic product rose at an annual pace of 2.1% in the quarter, up from the 1.5% rate it reported last month.
Oil prices rose sharply on concerns that there could be more uncertainty in the Middle East.
Brent crude jumped by 2.5% or $1.14, to $45.97 a barrel, while West Texas Intermediate crude climbed $0.94 to $42.96 a barrel.
As a result, shares in oil firms rose, with Exxon Mobil up 2% and Chevron 1.5% higher.
Boyhood, a film 12 years in the making, has won top honours at the New York Film Critics awards.
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(Close): Shares of the two newly split Hewlett Packard companies diverged after its last report as a consolidated company.