I am applying for a job at a tech company with offices at Zurich and Munich. I understand I dont have the job yet so I may be jumping the gun, but I was asked my preference. I dont intend to live long term/settle in these places, so retirement benefits against higher taxes and long term health benefits are not a major criteria. I am looking for a way to evaluate the compensation at both these places. Also as a side question, is it polite to raise these concerns to my recruiter and ask for advice?
As a practical matter this all depends upon the company, so in all honesty only they can give you a real answer. Some companies adjust salaries according to location (local law, tax rate, expenses, ...) others don't.
If you're dealing with a recruiter it's perfectly polite to ask for advice. But there's no guarantee that you'll get a straight answer or even if they know the answer. The one question that the recruiter should be able to answer quickly, if you don't already know, is the salary expectation at each location.
Research and research some more. You need to have enough knowledge of the tax rates and expenses in each location so that you can determine if one offer or location is better for you than the other.
The government websites for each location would be a good starting point.
If and when you get to HR I'd think it would be perfectly acceptable to ask the HR representative about this directly. They deal with it on some level already so should have the background to point you in the right direction.