You might try out of town a bit. We have stayed in the Hotel zur Gred in Freising and liked it.
http://www.hotelzurgred.de/
Freising on the München Sbahn system and is serviced by local (RB) trains. The hotel is very near the train/SBahn station. Freising is an attractive small town.
http://www.freising.de/
This year we are going to try Landshut and Hotel Restaurant Weihenstephaner Stuben, also near the train station.
http://www.weihenstephaner-stuben.de/
http://www.landshut.de/
For transportation to München for sight-seeing, you could either use the Bayern-ticket on the trains or the München Partner Card on the SBahn, both all day tickets.
Good Luck, Gary