I've been to the Christmas Markets in Munich twice. I highly recommend the Platzl Hotel (https://www.platzl.de/en/). It is a couple blocks off of the Marienplatz and around the corner from the Hofbrauhaus. We went to Nürnberg as a day trip from Munich.
For Bratislava, we stayed at the Raddisson Blu right on Hviezdoslav Square (https://www.radissonblu.com/en/hotel-bratislava). You literally walk out the front door into one of the markets. Perfect location. The rooms were a little dated but we were there 3 years ago and they were updating then.
In Prague, we've stayed twice and loved the Hotel Pod Věží (http://www.podvezi.com). (We will be back in two weeks) It is located immediately off of the Charles Bridge on the castle side. One of my favorite hotels in Europe. (We've already booked for this December when we'll be back for the Christmas Markets.)
I'm surprised you're not going to Vienna. Vienna actually has 8 or 9 small neighborhood type markets scattered throughout the central area of the city and a huge one in front of the city hall. Truly amazing! BTW Bratislava to Vienna is a little over an hour apart by train.
Have you looked at your timeline and travel route? If it was me, I'd probably fly into Prague and out of Munich. By train it would be easy to do Prague - Bratislava - Vienna - Salzburg - Munich. You could day trip to Nürnberg. Graz is easy to get to from Vienna but not so easy to Salzburg. Dresden is pretty far north and would be pretty out of the way.
Depending on how long you have, or maybe for your next visit, consider Strasbourg, France (which has had a market since the 1500's - https://noel.strasbourg.eu/en/les-marches-de-noel). You can easily fly into/out of Frankfurt (which has a nice market as well) and train to Strasbourg. The Alsace markets at Colmar, Riquewihr and Obernai are very nice and can be visited in 1-2 days. Strasbourg is a great place to visit.
One final piece of advice, check what date the markets open. Each city often has different dates.