Boston has been the second biggest VC market (counting the Bay Area as one) but every report I've seen shows New York has tied or surpassed Boston over the past few years.

http://mashable.com/2013/02/21/top-cities-startups/

http://mycrains.crainsnewyork.com/stats-and-the-city/2011/te...

http://www.cbinsights.com/blog/venture-capital/tech-venture-...

http://www.bizjournals.com/boston/news/2011/10/13/mass-drops...

From the last link, dated October 2011:

"Still, for Massachusetts to fall behind New York in VC financings is noteworthy, said Anand Sanwal, CEO of CB Insights. New York had already been leading Massachusetts in VC for tech — including Internet, mobile, software, hardware and electronics — since the second quarter of 2010. But due in large part to health care VC activity in Massachusetts, the state had remained ahead of New York in overall VC until the third quarter."