The thrilling race wasn't decided until the final few meters.
The 29-year-old broke the American record with a time of 31:37.
Huddle is the first American to win the New York Mini 10K since 2004.
The race around Central Park will take place June 14.
Ben True wins a stacked men's 5,000m; Molly Huddle runs second-fastest 10,000m ever for an American woman.
Mario Fraioli provides an update from the finish line on Boylston Street and recaps the B.A.A. 5K and Invitational Mile.
Huddle lives and trains 40 miles from Boston in Providence, R.I.
Track specialists Molly Huddle and Sally Kipyego will make their half-marathon debuts on the women's side.
She set a world's best 12K time last weekend in Alexandria, Virginia.