Northwestern (5-0) used a 14-4 run early in the second half to take a 46-36 lead over the Seawolves (2-3). Stony Brook got within 55-52 with 2:47 remaining, but Northwestern's JerShon Cobb sank a 3-pointer to push the lead back to six.
Stony Brook scored the game's first eight points, but the Wildcats' 14-0 run midway through the first half put them ahead 20-13. Northwestern led 30-28 at halftime.
Drew Crawford had 12 points and seven rebounds for Northwestern.