No question given a choice between Nuremburg and Munich that Nuremburg is the best choice. I'm not so sure I'd weigh Munich less than Frankfurt though. I know coming from Boston that Munich is the better choice for me over Frankfurt for a couple of reasons.
Firstly I think it's easier to get from Munich to Bamberg if you are considering a one day car rental to do so. With multiple people this might be the cheaper option and it's not a bad drive and easy to drop the car off in Bamberg when you arrive. It was actually quite pleasant driving through the Hallertau hop region on the way up. Driving from Frankfurt .... forget about it, it was a nightmare the one time I tried that trick.
Secondly I found the flights leaving Munich to be much later in the day than Frankfurt and this made it a lot easier to enjoy one last night in Bamberg and not have to get up too early.
I would also say I personally like the Munich airport much better than Frankfurt. I found it a lot less crowded and easier to get around. Frankfurt was a total zoo when I flew out of there last December. Munich even has a beer garden at the airport (unfortunately the beer isn't so good) but still it's better than waiting at the gate.