Wheaton (4-0) used runs of 13-0 and 11-2 in the first half to take a 37-21 lead at the break.
In the second stanza, the Thunder maintained a double-digit advantage until the 6:34 mark when Brandon Woodhead's basket cut the gap to 54-46.
Chicago closed to within six points of the Thunder, 54-48, with 5:50 to go on a pair of free throws by Justin Waldie, but the Maroons could get no closer.
Wheaton hit nine of 10 free throw attempts in the game's final two minutes to seal the victory.
Waldie was the only Chicago player to reach double figures with a game-high 18 points.
Jon Nielson and Martin Trimiew finished with 11 and 10 points, respectively, for Wheaton. The Thunder shot 48.0% from the floor to 34.3% for the Maroons.