I rent cars occasionally and have found that Philadelphia has good prices. New York tends to be quite high. The difference may or may not be significant to you but if you can as conveniently and cheaply fly to PHL (or probably Boston, or Washington) I would try that. Personally I use Expedia, trying one location at a time, when deciding where to book from - obviously the differential will vary depending on when you are traveling.

(This Sunday, which was a holiday weekend, I needed a one-day rental and reserved at LaGuardia. The rental company - Dollar - somehow had no cars to honor my reservation when I got there, and the only company that had unreserved cars available - Enterprise - charged a ridiculous price, which I nonetheless paid with the rationalization that it was just one day. Since I ordinarily avoid renting from NYC I don't know whether that was just a freak occurrence or what, but I am planning on returnng to my policy of not renting in NY.)