Thompson's free throw with 3:10 remaining put the Broncs (11-9, 6-2 Metro Atlantic Athletic Conference) ahead to stay, 60-59.
Tavon Sledge's layup for Iona had tied the game 59-59, ending a stretch of 5:14 without a field goal for the Gaels (12-7, 6-2).
Iona's total matched its season low. The Gaels, who had won six straight, were averaging 82.6, third highest in Division I.
Pereira made his second straight start in place of Nurideen Lindsey, who is recovering from a concussion, and hit two 3-pointers 14 seconds apart, when Rider erased a 25-14 first-half deficit to lead 35-30 at halftime.
SMU has signed a second player from Australia, 6-foot-11 forward Harry Froling, to a national letter of intent. The Mustangs previously signed guard Tom Wilson from Australia.
There's nothing to suggest the Jayhawks won't end up atop the Big 12 for a 13th season in a row. But what about a return to the Final Four?
Colorado State graduate transfer John Gillon has chosen Syracuse, giving the Orange a potential starter at point guard entering the 2016-17 season.