I lived off my savings during this time. Some people took loans (see the Harvard Ext postbac thread for details). Since you have the option of living at home in NYC, moving to Boston+paying rent+Harvard Extension may end up being about as expensive as NYU/Columbia. You'll have to do the math to see what works out best for you. If you are currently working, SAVE UP! You'll have to get ready to give up a large chunk of your social life in postbacc, then almost all of it in med school.
I followed the two year program at Harvard Ext. They start us off with Gen Chem and Physics (not Bio). I thought this was somewhat odd, but it made sense. For a lot of people, I think Gen Chem will be the easiest of the 4 pre-reqs and Physics/Organic Chem are the hardest. If you took Bio/Gen Chem first, you end up lumping the two hardest classes together in the second year (you'll also be studying for the MCATs). Also, Gen Chem and Physics are the two math-intensive courses (there is no math in Bio or Organic Chem), so if you can't cut it with math, it's good to know up front rather spending the money on a 2nd year of postbacc. Having said this, I'm sure plenty of people pull off Bio/Gen Chem in the first year just fine, but doing Gen Chem/Physics makes more sense to me now.
According to SUNY, to maintain NYS residency, you must maintain at least 3 of those listed under the "Proof of Domicile" in this document:
http://www.suny.edu/sunypp/documents.cfm?doc_id=402
Therefore, you can go to school elsewhere for 2 years and still have NYS residency if you can maintain that proof.
If you end up sticking with CUNY, but get closed out on classes, try emailing the professor of the course. Professors can grant "overtallies", but realize that this is more difficult with classes that have labs (all the pre-reqs) since there are limited lab resources compared to lecture hall seats. After I completed my postbacc requirements, I took biochem at a CUNY during my glide year. The class filled, but I emailed the professor and was allowed to take the course. I know a few med student classmates who did their postbac at CUNY (mostly Hunter), so it's do-able. Hunter has a postbacc certificate program. I believe if you are part of the program, you get slightly earlier registration dates, but still after the undergrads.
Important Addition: Also, check now to see when you would likely take the MCATs. They are changing the MCAT format to include other subjects some time in 2015 (check to be sure), so you may need more pre-reqs than the standard Bio/Gen Chem/Orgo/Phys if you fall after the MCAT format change.