Carson Puriefoy made two free throws to give the Seawolves (5-6) a 59-58 lead with 1:30 remaining. Both team missed shots on their next possessions before Williams' basket. Puriefoy missed a 3-point attempt with four seconds left and Jamal Reynolds grabbed the rebound for the Golden Griffins (5-4).
Lewis led Canisius with 16 points. Reynolds added 11 and had a career-high 17 rebounds.
Warney had 19 points and 18 rebounds for Stony Brook. Puriefoy added 15 points.
The Seawolves have lost four in a row, all on the road, for the first time since 2007-08.