Stony Brook (13-4, 4-0 America East) won its ninth in a row, while New Hampshire (8-8, 1-2) has lost two straight and four of five.
Jacoby Armstrong's jumper put New Hampshire up by one with 14:34 left in the first half, but it was the Wildcats' last lead of the game. Stony Brook used a 20-5 run over the next nine minutes to put the game out of reach and led by 19 at halftime.
The Seawolves were never seriously threatened in the second half.
Armstrong led the Wildcats with 14 points and nine rebounds, and Iba Camara went 6 of 9 with 13 points.
Stony Brook held New Hampshire to 32 percent shooting from the field and forced 14 turnovers.