We will be traveling from Prague to Munich by train the day before our flight home. Is it best to stay at an airport hotel or one with shuttle to airport? Does the train go all the way to the airport or do we need to transfer at Munich HBF? Any hotel recommendations? Thank you.
If you want go all the way to the airport you will have to make at least one transfer somewhere, not necessarily Munich HBF.
It depends on what time you book.
I'd opt to stay at an airport hotel and then venture into Munich from there if you want to.
That train stops in Freising, a nice historic town near the airport with good bus and train connections to it. I'd spend the night there or in Neufahrn (Gasthof Maisberger at the S-Bahn station; good restaurant). Those airport hotels tend to be expensive (Hilton) and / or soulless.