Could you share which areas? I've been exploring NYC as well but have yet to stumble upon any areas that match what you described.
If you choose to live close enough to a train station, almost everything of interest is within 20-40 mins by train. Subway is not exactly great, but it's safe and works around the clock in most places. (To say nothing of the fact that in most places the daily necessities are within walking distance, even in not-so-dense Brooklyn.)
It makes places in Brooklyn, Queens, New Jersey, and Long Island accessible with a reasonable commute.
Even in Manhattan, though, the rents are similar to SF but we've found you get slightly more for it.