Lynn was 6 of 10 from 3-point range and Willis was 4 of 6 as the Highlanders hit 13 of 22.
It was the first of six straight home games for NJIT. The Highlanders next road game is their regular-season finale against Howard on Mar. 4.
Reginald Johnson hit five 3-pointers and finished with 27 points for Hampton (8-14). Deron Powers, Jervon Pressley and Quinton Chievous had 11 points each as the Pirates had their losing streak extended to six games.
NJIT made 17 of 32 field goals (53.1 percent) in the opening 20 minutes and held Hampton to 36.7 percent for a 45-29 halftime lead.