Biotech ecosystem is better in BOS and maybe finance-related stuff in NYC, but otherwise I agree with you.
The biggest difference between BOS and SFO are the big biotechs. SFO has one (GNE), while BOS many.
That's debatable. I think Boston and the Valley are about the same (with the Valley maybe a little ahead) for biotech. Either way, Boston (as a city) is depressing as fuck, so I would avoid it like the plague.