Having lived in both NYC and the Bay Area for extended periods of time, I would say that at least in terms of rent and location, that there are many more option

Having lived in both NYC and the Bay Area for extended periods of time, I would say that at least in terms of rent and location, that there are many more options for running a start-up cheaply in the Bay Area. You might be able to find a decent deal on housing in, say, Astoria, but if you look in Silicon Valley, Berkeley, Oakland, or even certain areas of SF, you'll find many cheaper options that give you twice the space and are just as conveniently located.