For me:
content where you are = content wherever you are, no matter where that is, now and in the future.
content with where you are = content where you are right now
Also, I would use them in slightly different contexts.
Sarah: Do you want to come and sit on the sofa? You look uncomfortable on the floor.
Helen: No, thanks. I'm happy where I am.
Sarah: Are you happy with your life? You're single, with no kids, you don't seem to have many hobbies, and your job doesn't seem very satisfying.
Helen: I'm happy with where I am.