Mutai also won the 2011 championship, making him the first to win back-to-back New York Marathon titles since John Kagwe of Kenya turned the trick in 1997-98.
Last year's marathon was canceled in the wake of Hurricane Sandy.
Mutai finished first in a field of more than 45,000 runners, clocking in with a winning time of 2 hours, 8 minutes and 24 seconds. Cold and windy conditions prevented him from bettering his 2011 time of 2:05:06.
He was an easy winner, finishing 52 seconds ahead of Ethiopia's Tsegaye Kebede.
Jeptoo, meanwhile, recorded a time of 2:25:07. Coming off an April win at the London Marathon, she passed then-leader Buzunesh Deba of Ethiopia with about 2 miles remaining and went on to the victory.