I've built startups in both Boston (primarily) and NY (a few years). The industry-focus is certainly one element of it, as others have mentioned.
Overall, NY is bigger. Bigger everything. So you get more great people, plus a ton more mediocre people. The expats from finance wanting to get in on entrepreneurship and startups shapes the flavor of things a bit. Means more money floating around, but also more finance people floating around. :-)
I find there are more solo founders and smaller teams in Boston, and I wish that Boston entrepreneurs were better about partnering up with 2-3 great people instead of worrying about founder equity stakes as much.
Boston has some great and growing companies, and the startup community is incredibly strong and tight. It's a great place to come to get indoctrinated into that scene in a way that would be a challenge just starting out in NYC.