Thomas scored 12 points and grabbed a game-high 11 rebounds for Bowling Green, while Otis Polk chipped in 11 points.
Brown's jumper early in the game helped push the Falcons to a 9-0 run to start things. They stretched the lead to 25-8 midway through the first half and were never threatened.
Bowling Green led by 25 points at halftime and held on despite being outscored 46-38 by the Crusaders in the second.
Brandon McPherson paced the Crusaders (15-15) with 16 points.