I can recommend the Hotel Haberstock which is about 2 blocks from the Hauptbanhof (main train station).
A 5 minute walk to the Marienplatz, 10 minutes to the Hofbrauhaus and Viktalmarkt. We stayed there and it is clean and the breakfast is great with lots of choices: delicious fresh crusty breads and rolls, pastries, eggs/omelets made to order, cereal, fruit, yogurt, cold cuts and cheeses, juice - most days we filled up on breakfast and skipped lunch!
The location is wonderful - each day we took the train to a different location and when we came back each night it was a quick walk to the hotel.
The only problem is that there in a bar on the street across from the entrance that did get noisy at times but we kept our windows closed.
Make sure you check into a Bayern Pass - it is good for two people for one day on train/buses, trams, etc. as long as you stay in Bavaria, the southern part of Germany. We bought one each morning and went to Augsburg, Nuremburg, Rothenberg, Neuschwanstein Castle. They print you out an itinerary that is very helpful and it cost us something like 14 Euros each per day. There is a time restriction - you can't travel before 7 AM I seem to remember but that was no problem, lots of train run all day and are super efficient.. If you have time, go to Rothenberg, its a bit far but definitely worth the trip and your Bayern Pass will cover the train. Medieval village that will take your breath away - was never bombed during the war. Tiny cobblestone streets, lovely churches, utterly charming.