Albany (10-7, 5-0) took the AEC title with a 69-60 win in March and led the rematch wire-to-wire for a fifth straight win.
The Great Danes took a 31-25 lead at the half and expanded it to 14 points on a layup by Richard Peters with 12:40 to play. Stony Brook scrambled back, cutting the lead to 53-47 with under three minutes to play, but Albany closed the game on an 11-0 run.
Sam Rowley finished with 16 points and 13 rebounds for Albany, which held a decisive edge from the free throw line. The Great Danes were 19 of 23 while the Seawolves were just 5 of 11.
Jameel Warney scored 16 points to lead Stony Brook (12-8, 3-2).