Mutai smashed the New York Marathon course record with a time of two hours, five minutes and six seconds, shattering the old standard of 2:07:43 set by Ethiopia's Tesfaye Jifar in 2001.
Emmanuel Mutai, the reigning London Marathon champion who is not related to the winner, was second for the second year in a row in 2:06:28 with Ethiopian Tsegaye Kebede, the 2008 Beijing Olympic bronze medalist, third in 2:07:14.
Geoffrey Mutai, 29, ran the fastest marathon time ever recorded to win this year's Boston Marathon men's crown in 2:03:02 but the time is not recognized as a world record by the IAAF because of course elevation issues.
The men's leaders stayed in a pack of about 20 runners early in ideal conditions, but after 25 minutes the Mutai duo picked up the pace and trimmed the lead group to 10 on course-record pace, reaching the midpoint of the 26.2-mile journey in 1:03:16.
Ninety minutes into the race, Geoffrey Mutai pulled away racing up First Avenue and no rival could answer his challenge.
The winner was still 88 seconds off the men's marathon world record of 2:03:38 by Kenya's Patrick Makau at the Berlin Marathon just 43 days ago.
Kebede, the 2010 London Marathon champion, was followed in fourth by the 2010 New York winner, Gebre Gebremariam of Ethiopia, in 2:08:00 with Moroccan Jaouad Gharib fifth, another 27 seconds back, and Eritrea-born American Meb Keflezighi, the 2009 New York champion, sixth in 2:09:13.