I'd definitely go for Munich. As a matter of fact, I already do study in Munich.
Check the international ranking:
Munich is 27th (Technical University) and 35th (General University), while Vienna is 41th and Frankfurt 68th.
No need to say that rankings are not the only thing that matter.
Student life in Munich is absolutely fantastic. Here's why:
* The student town. About 2500 Students living there. ONLY students. With parks, clubs, bars, gyms, ... Just imagine.
* Number of students. About 100.000 students in a city of about 1,3 Mio. In summer you'll find them in a park (English garden), playing soccer, making bbq or just chilling. In winter going skiing or any indoor activity imaginable.
* Munich culture. Very laid back, sitting in beer-garden, ...
* Leisure time. Munich offers every activity imaginable. Sports, watching sports, museums, concerts, and so on...
* Oktoberfest. No need to say more.
* Jobs. There are plenty of jobs for students. Huge companies have their headquarters in Munich. Allianz, BMW, Siemens, Infinion and many more smaller ones.
I really love Munich.