I know, I know, Pete's isn't in NYC, but they make, beyond a doubt, the best bagels I have ever had. I live in Brooklyn, and yet every time I go to visit my mom in Rockland County, I go to Pete's. They've got the only bagels I've ever eaten that don't need anything at all on them -- even the plain ones. And if you're lucky enough to get 'em straight out of the oven (not tough on weekends, since they make them constantly), it's pure heaven. Pete just needs to open a branch in Manhattan or Brooklyn so I can get them all the time!
Pros: Best-ever bagels
Cons: There's usually a line, but that's just because it's so good