The problem is time. I live in Bedford, and while it's technically possible to get a bus+subway from here to the financial district, it takes about an hour and a half. That's compared to 35 minutes driving (no traffic), ~55 minutes driving (with traffic), an hour driving to Alewife then taking the red line in, and an hour and a half for biking to Alewife and taking the subway in. Not much point.
Commuter rail is similar - it's like 1.5-2 hours to take the commuter rail from Concord to Porter and then transfer to the red line. Might be a bit better closer in to the city, but commuter rail coverage is a bit spotty - it's faster to drive to Alewife from Bedford than it is to get to the nearest commuter rail stations in Concord or Lincoln.
I had planned on taking the Lowell train to Boston after I moved to NH, but that was when gas was $3.50+ a gal and it would have cost me $25 for gas round-trip. Commuting on the train would have added about 2 hours a day to my commute vs driving in.
My work allows me to be very flexible with my schedule, so I've been driving in later to avoid rush hour and leaving work after 8pm. With gas less than $2, it costs me less to drive in than it does to take public transportation, plus saves me 2 hours a day.
Time = Money (or sanity, at least).
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.