I went to the Beethoven-Haus in Bonn. It was interesting – the house has been turned into a museum with music and pictures and other memorabilia. (my favorite was an ear trumpet). The coolest part, I thought, was the computer room where you could listen to Beethoven’s music while following along on images of his handwritten scores.
I’m just a Beethoven fan, not anything near an amateur scholar, but I enjoyed the museum, so I’d imagine that you would enjoy it even more. Also, I haven’t been to Vienna so I can’t compare.
If you go to Bonn, you should also check out the Arithmeum – a museum devoted to the history of math with a huge collection of historical calculating machines.