Emile Blackman's dunk cut Niagara's deficit to 62-61 with 2:36 left. Manhattan's Rich Williams made a steal and found Zane Waterman for a layup and, after Waterman drew a charge on the other end, Tyler Wilson made one free throw for a four-point lead with 40 seconds left.
Niagara was whistled for another charge and Stores hit two from the stripe before Karonn Davis' 3-pointer cut it to 67-64 with four seconds left. Stores sealed it at the line.
Stores hit three from distance and had 15 points for Manhattan (7-10, 4-4 Metro Atlantic Athletic Conference). Waterman and Williams added 12 points apiece.
Matt Scott had 21 points and eight rebounds for Niagara (5-14, 3-5), which shot 49 percent from the field, but just 2 of 12 from 3-point range.