I had offers in both SV and Boston and it was a tough choice. I'm still not sure I made the right one.
While Boston is cheaper, it's not that much cheaper. I think you'll probably do slightly better off depending on the offer you get. (I currently live and work in Mountain View)
Startup-wise Boston seemed pretty sparse compared to the Silicon Valley. That was definitely part of my decision (not just where to work, but as you say, networking, conferences to go to, etc).
I still think little fish, big pond is the better way to go. It gets frustrating otherwise and limits your growth. Important team in a less known company also is much better for career and personal satisfaction.
I'll be honest, weather also greatly influenced my decision. Also what's your move going to be like? Getting all my stuff across the country was yet another reason for me to stay in the SV.
I personally actually much prefer Boston city and the general vibe of Boston, but career-wise I decided SV was better.