The Yarn Co. is on the second floor of a building on Upper Broadway - I have to admit, I get claustrophobic there, but they have a lot of stuff crammed into a very small space! Purl Soho is lovely, and I like the atmosphere there. Knit New York seemed small (but has a snack counter!) - I didn't spend much time looking there. Knitty City (on W 79th) is nice, too, but I'm not sure they carry individual patterns - or if they do, they're not making it obvious where they are!
But again, a nice atmosphere. And I have to say, the times I've been in these places, the people working there have always been pleasant - always a big plus!
Hope this helps... unfortunately, I didn't take up knitting until I left NYC (
), but I go home a few times a year and my mother and I sometimes go out to a new LYS to check it out. Still haven't been to Seaport Yarns or the Point, but those are on my mental list...