Boateng has been strongly linked with a move to Paris Saint-Germain and Hoeness said earlier this month that the chances of a deal happening were "50-50".
The Germany defender has told Bayern of his intention to leave but PSG has bolstered its defence with the signing of Thilo Kehrer from Schalke.
And Hoeness now believes Boateng will be with Bayern throughout their first campaign under new coach Niko Kovac, who has said he wants to keep the centre-back.
"If you want to hear my feelings tonight, I would say that he will stay in Munich," Hoeness said.
Boateng played the second half of the game as Bayern ran out 4-0 winners against Schweinsteiger's MLS side Chicago Fire at the Allianz Arena.