I just returned from a week in Berlin, and have also spent time in MUC and other cities and towns in Germany. I vote for both if you can do it. Berlin for the incredible recent history presented in awesome museums, monuments and displays (Checkpoint Charlie is one not to miss). The modern architecture is splendid, great restraurants with world cuisine, excellent shopping. Munich is lovely, can't put it better than others have here. Take the ICE train and see the intervening countryside (albeit quickly). Really, you will love anywhere you go in Germany; I always do.