We've invested in both San Francisco and New York startups, and New York impresses me more and more in terms of ideas and quality of the startups. But I've still got to give the clear advantage to San Francisco simply because of the network (investors, other entrepreneurs, schools, bloggers, etc).
I think there's something to Branch CEO Josh Miller's notion of New York "keeping things real", as it were -- but I also think that may lead to more hardship that simply isn't necessary.