OK, I am still debating whether to take the train or bus. However, if I take the bus, where does it leave from? I have seen several comments that it now leaves from the bus station but Rick's Germany 2014 book says the train station since it is run by Deutsche Bahn, the train company. Which is correct?
I look on the Deutsche Bahn website. Some of the buses run from the bus station at Hackerbruecke, and some say from the Hbf. I am looking at May 8 and all the buses say Muenchen ZOB Hackerbruecke.
The buses leave from the Hackerbrücke ZOB (Zentral Omnibus Bahnhof). It's about a km west of the Hbf, the next stop after Hbf going in the direction of Pasing. Here is a map showing the routes of all the IC buses run by the Bahn. And here is a map showing the location of the Hackbrücke ZOB and the Hbf in Munich.
An important thing to know here is that if you specify "Muenchen Hbf" as from: when booking, the ticket will be from the ZOB, and technically you would have to walk from the Hbf to the ZOB or buy a separate ticket for the S-Bahn. However, if you write out "Hauptbahnhof" (or select it from the pulldown), the ticket will include the S-Bahn (and you can use any of them, S1 - S4, S6 - S8) from the Hbf to the ZOB.
For some reason, the Bahn no longer sells advance purchase Savings Fare ticket from Munich to Prag by way of Nürnberg (ICE Munich - Nürnberg, IC bus Nürnberg - Prague).
Thanks to the both of you for the info.