Keitany, victor of this year's London Marathon and the fastest ever in a women's only marathon, had been expected to run away with the race but a slow pace allowed Flanagan and others to stay with her early.
Flanagan posted an unofficial time of 2 hours, 26 minutes, 53 seconds.
NEW YORK (AP) - Geoffrey Kamworor of Kenya has won the New York City Marathon, holding off countryman Wilson Kipsang by three seconds for his first major victory.
Kenya's Mary Keitany, who was chasing her fourth consecutive NY victory, was second with 61 seconds back.
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Kipsang, the 2014 NY champion, was three seconds back with Ethiopia's Lelisa Desisa third in 2:11:32.
On the men's side, Kenyan Geoffrey Kamworor beat out countryman and 2014 victor Wilson Kipsang for his first major marathon victory, with a time of 2 hours, 10 minutes and 53 seconds.
Only one other women's race runner - Norway's Grete Waitz - can claim that achievement, with five consecutive wins.
Flanagan placed sixth in the women's marathon in at the Rio Olympics past year, the top American finish.
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After taking the lead in the 23rd mile, the 24-year-old 2015 NY runner-up had to contend with Kipsang, whose final push brought him ever so close to his countryman.
Behind her, but fading fast, Mary Keitany was chasing history, too: The 35-year-old Kenyan had won this race three times in a row.
In the wheelchair event, the Swiss dominated with Manuela Schar tops among women and Marcel Hug finishing first among the men. Emmanuel Mutai from Kenya settled second in 2:03:13 followed by Ethiopian Abera Kuma in 2:05:56 and Kamworor 2:06:39.
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