For PhDs, I've heard the most important thing is research/advisor fit. With regards to reputation, MIT and Berkeley are pretty even (maybe MIT takes it based on name recognition), but what you do during your PhD will matter much more than the school name. And in that sense, having a good set of choices for your grad advisor is a big advantage from the get-go. Also remember, you can change advisors mid-way, and having a number of people you'd like to work with is a big plus. As for the location preference I can certainly understand that sentiment. Maybe it might be worthwhile trying out something new in terms of scenery?
It's a pretty good dilemma to have, though. Congrats!