Ladies, please forgive the forum crash. I started composing this as a PM but thought others might benefit.
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I "sorta-kinda" relocated to the area a few months ago - I took a job in Lower Manhattan and relocated to southern Fairfield County, CT.
Affordable neighborhoods: Depends on where you work. A lot of my coworkers live in New Jersey. A lot of my neighbors in Connecticut work in Midtown. I have yet to meet anyone else crazy enough to commute from Connecticut to Lower Manhattan.

In general, the farther from Manhattan you get, the less expensive the housing, but there is a tradeoff in the form of a longer commute, higher crime rate, poorer school system, etc. There are also many wealthy enclaves here and there in the suburbs, where housing is very expensive even though the commute is long.
Subway system: I've found it's just like learning the best way to get around by car in a new town. First, you learn how to get to work. Then you refine that route (e.g., do I get off the subway at Fulton St. or Wall St.?). Then you start to learn how to get to different neighborhoods to visit friends or go to certain restaurants or tourist attractions.
I don't live in NYC, so I can't comment on what it's like living there or what the social scene is like.
NYC is an amazing city... there are few places with such good job opportunities, and few places with such good access to cultural activities such as museums and theatre.