I faced this exact dilemma last year, and I picked Durham, albeit a little reluctantly. However, I'm six months into my first year and I ADORE Durham. I managed to purchase my first home in a great neighborhood, I get to experience enough wintry weather to get a taste for it but not hate half the year, and there is never a shortage of things to do in the area. Had I chosen Boston, I would have had at least one roommate, even with the generous stipend offered by the school there, and I would have become all too familiar with crap-tons of snow. That being said, I'd still love to live in Beantown some day.
So, I guess my comment might not be that helpful. I just wanted you to know that Boston's a great city, but Durham has many charms too. And while it's hard to compare a city of ~250,000 with a metropolitan area of 4.5 million, I think Durham has a lot to offer.