I have been to Munich 5-6 times over the last 10 years. As it is usually my arrival or departure city, I have nearly always stayed near the Central Hauptbahnhof for late night or early morning train connection convenience. While there are many nice hotels there, the area is a bit gritty, although perfectly safe.
I would actually prefer either the Alstadt, as a previous poster recommended, or something around Marienplatz. There are some very nice places near Viktualien Market as well.
I agree that the Augustiner Beer Hall is a better choice for food and beer but you really should not miss the Hofbrau Haus either. If you are willing to face some difficult realities, the Dachau museum is transformative.
As a side note: we always end up spending a day shopping before we fly out. The last time, my wife had to buy another suitcase.
