Congrats on your acceptances, I envy your options! Maybe I am just old-fashioned but I was under the impression a phone call followed by a formal letter was the proper way to reject an offer. Not at all trying to get onto you, but I thought e-mailed declines were considered rude.
To answer your question, I would compliment their program and site "neutral" reasons for declining (e.g., geography vs. other school, family). The only reason I would stay away from any criticism is because I assume the school you rejected is still in your area of interest and you will probably work with these people in the future. I'm sure some will disagree but I would play it safe.