Mutai finished the course in one hour, 50 seconds. Britain's Mo Farah, a double Olympic track champion, came in second. He recovered after tripping up between fifth and sixth mile.
Kenya's Stephen Sambu was third, a second behind Farah.
Sally Kipyego was the women's race winner, at a time of one hour, 8 minutes and 31 seconds. Ethiopian Bizunesh Deba, who lives in the Bronx, was second and American Molly Huddle was third.
20,000 runners took part in the race, which looped around Central Park before heading downtown through Times Square to Lower Manhattan.
Crowds waited to cheer them on in Times Square, which is in the center of the 13.1 mile course.
The weather was chilly for this year's race, with temperatures in the 30's.
This year's field was the largest ever. The oldest man running was 81, and the oldest woman is 82. The youngest runner was 13.
The course was reconfigured this year to accommodate an increase in the field size to 20,000 runners and allow for the addition of a professional wheelchair race.