Warney, who was 10 of 13 from the field overall, had 12 points and eight rebounds in the first half as Stony Brook built a 41-24 lead. NJIT was just 6-of-24 shooting (25 percent) in the opening 20 minutes.
Four of NJIT's six made field goals to start the second half were from 3-point range, but the Highlanders still trailed 65-40 with 12:18 left.
Ahmad Walker recorded his second straight double-double with 15 points and 11 rebounds for Stony Brook (8-4). Carson Puriefoy and Bryan Sekunda also scored 15 apiece.
Chris Jenkins made five 3-pointers and scored 15 points for NJIT (7-6), which was outrebounded 37-24 and turned it over 16 times. Tim Coleman added 12 points and Ky Howard had 10.