I wish I could avoid the subway! But unfortunately, it's the easiest way for me to get around. Dealing with the unpredictability, dirtiness, and crowding on the subways can suck at times, but it's a good and cheap way to get places around NYC. I think if I could consistently get a seat every day during my commute (so I could get some quality time knitting or sleeping), I'd like the subway a whole lot!
My favorite yarn store so far is Knitty City - the staff are soo friendly, the store is very spacious, and the yarn selection is pretty good. I like School Products for the yarn, but it wouldn't be good for knitting support. If you want to know my least favorite yarn store, I can tell you that too.
(although I've seen it covered extensively on forums already, hehe)
I have yet to check out Downtown Yarn, along with Seaport Yarn and Brooklyn General..