If you like the quiet life, lots of academic options, and very tame social gatherings then Boston is for you. If you like excitement, extraverted social culture, and lots of new experiences then I'd look at SF.
Boston has some plusses: it's a walking city... possibly the only true walking city in the country (of any size). You do not need a car. It's ridiculously safe for a big urban area. Bostonians' idea of a bad neighborhood is one without a Starbucks in eye-shot. It's very economically healthy and has a lot of good high paying techie jobs.
But some of that could be said about SF too... just not the walking city part. (Well, SF proper can be handled without a car, but all the techie stuff is in the valley which is a car-centric suburb.)
Both are among the nicest cities in the country.