Daniel Stewart added 14 points and 14 rebounds for Rider (17-13, 11-6), which previously defeated Niagara 72-69.
Niagara (17-12, 12-5) took a 44-42 lead on Juan’ya Green’s layup midway through the second half. But Thompson hit a 3-pointer on Rider’s next possession and the Broncs scored the next 10 points to pull away.
Thompson capped the run with five straight points and Niagara never got any closer than five the rest of the way.
Rider, which has won four straight and six of its last seven games, currently sits a game behind Niagara in the MAAC. The Broncs can still win the regular season title with a win against Canisius on Saturday and losses by the Purple Eagles and Loyola (MD).
Green paced Niagara with 27 points.