In the more urban programs that I considered (and eventually matched with one), training tended to weigh more heavily on inpatient acute care then outpatient neurology. Often you had additional experiences working in county hospitals as well as VA hospitals and I really loved having that breath of exposure. And I love cities.... I admit though.... my outpatient training was lackluster during residency, and that is what most people do primarily in their Neurology careers. Keep that in mind as you go through residency, and as you decide on your direction... make sure you get enough exposure to things that your residency lacks during electives, if you can.
The city I was in was very very expensive, although still not as pricey as NYC. Remember, when people are talking about great subsidized housing at Cornell, it is a relative statement. NYC is staggeringly expensive, but when I walked into the studio apartment that I would be eligible for as a single resident at Cornell, I realized I would have to leave behind half of my belongings and live in a tiny apartment with no charm... location location location.... Definitely ok for some, but a little tight for me. If you come in as a couple, they (Cornell) would probably offer you a one bedroom... couples have it better.
Actually, you will be in a better position then most cost of living wise by living with your girlfriend. Two can live much more cheaply then one. I lived quite well as a single on my resident salary (which was not great for my pricey area), because I didn't have loan payments (MD PhD program alum). But when I saw how my married classmates lived, I felt like a frugal student.... They could afford much nicer places to live then I could, and I still paid a much higher percentage of my salary on rent.
Boston is a wonderful place to be in medicine/academia at some point in your career, and a great city to live in that is very manageable. Too bad it has gotten pricey.... but again... as a couple with your girlfriend bringing in an income, you should be fine.
I think cost of living will be less of an issue. The major issue I would think will be for your girlfriend being able to accommodate to your busy schedule and fatigue.