Four McGlynn had 14 points, the only 43 victory over Stony Brook.
Sandro Carissimo registered eight points and five rebounds for the second- seeded Catamounts (23-11), who are advancing to the NCAA Tournament for the fifth time in school history despite not converting a field goal for nearly the final 10 minutes of the game.
Vermont's Brian Voelkel dished out seven assists and pulled down 15 rebounds.
Al Rapier and Dave Coley scored 10 points apiece for top-seeded Stony Brook (22-9), which lost in the conference's championship game for the second straight year.
The Seawolves were unbeaten (13-0) at home this season. But each of those wins came at Pritchard Gym. Saturday's contest was played at Stony Brook Arena.