In Munich, my teen boys enjoyed:
Allianz arena tour
BMW museum/showroom
Olympic Park
Bike tour of Munich (more enjoyable than expected)
The stream in the English Garden (it was really hot)
Watching the surfers
Dachau Concentration Camp - took the tour in English offered onsite. It was unsettling but our guide was extremely knowledgeable and appropriate for our teens. I highly recommend it.
You probably know this, but the 9 Euro ticket is great for getting around Germany, minus the ICE trains.
We spent several days in Garmisch-Partenkirchen, a few hours away from Munich. It was beautiful and our boys' favorite part of the trip. We did:
Zugspitze peak via cable car. Can be accessed from Germany or Austria.
Lake Eibsee hike and the boys swam in the emerald green water. German Zugspitze cable car is accessed here.
Alpine Coaster in Oberammergau
Neuschwanstein Castle tour
Parnach Gorge
Alpine Coaster in Garmisch
Olympic Ski jump
I wouldn't make a separate trip for the last two but they were entertaining while we were there.
Mom to Two Wild and Crazy Boys and One Sweet Baby Girl