Not a cafe per se, but Jittery Joe's on 45th between 2nd and 3rd has the best coffee in the area hands-down. They french press all of their coffee... I don't know of any other spots in the city that do that (restaurants not included).
They have a few tables in there that are usually available and they get pastries from Sullivan Street Bakery, but it's kind of a dark spot.
Cool. I didn't know about Jittery Joe's. Seems like an odd place for NYC. They are into cycling, which is pretty cool. And are based in Athens, Ga.
They got a mention in the NY Times coffee article today and Macchiato (serious ommssion did not).
Also depends on what OP means by "cafe". Actually places like Macchiato (and presumably Jittery Joe's) are more like coffee bars. I think of cafes as the type of places that used to be common in the West Village and are now a dying breed. Table service with coffee and espresso drinks, desserts, light meals and sometimes beer and wine.