IMHO, you're right on all counts about the pros and cons. I don't have recent data, but my impression is that Boston rents are not significantly cheaper (as they would be in, say, Alabama); savings will come from transportation costs. You can live without a car in Boston. Living without a car in Silicon Valley will make you feel like a second-class citizen. Obviously, Boston is closer to your folks if you're from NY.
If I were going to do a startup, and was able to honestly utter the phrase "I lived in SV for a while and loved it"... it's very hard to argue with Silicon Valley. Yeah, it's a monoculture, but it's a monoculture designed around what you're trying to do. Aspiring screenwriters move to L.A.; aspiring musicians move to Nashville; aspiring software wizards move to Silicon Valley.
But the most important thing is: you can change your mind. More than once. Pick the job that seems the best and don't sweat it. Sample Boston for a year or two if you want and make the move to SV later.