The Seawolves (26-7), seeded seventh in their quarter of the bracket, will face Iowa in the second round.
Stony Brook earned an automatic spot in the NIT by winning the regular-season title in the America East Conference, but fell to Albany in the semifinals of the league's tournament.
The Seawolves took control against Massachusetts by holding the Minutemen scoreless for the final 7 minutes of the first half. Stony Brook scored the final 16 points of the period to take a 37-25 advantage.
Jackson and Coley combined to go 16-of-25 from the field. Jameel Warney added 16 points for Stony Brook.
Massachusetts (21-13) reached the semifinals of the Atlantic 10 Tournament before falling to Virginia Commonwealth. The Minutemen were paced by 16 points from Freddie Riley.