Sean Armand added 18 points for the Gaels (12-8, 9-2) who pulled even with Canisius for first place in the MAAC.
Iona went on a 7-1 run to take a 71-63 lead with 2:43 to play. The Gaels led by no less than six from there and made 7 of 8 free throws to secure the win.
Manhattan trailed 39-34 at halftime, but stormed back to take a 50-44 lead less than 6 minutes into the second. Iona answered with 12 straight points, capped by A.J. English's back-to-back 3-pointers to take the lead for good at 56-50.