Eater NY has compiled a list of 21 fine coffee establishments located in NYC.

There's a pretty handy interactive map to help locate the different establishments.

I can't vouch for most of the list, but I've been to and can personally recommend these from the 21 Eater chose, in no particular order:

• Culture Espresso: awesome chocolate chip cookies the size and density of NHL regulation hockey pucks;
• Joe (the art of coffee): good to go but I don't know any locations that have seating;
• Cafe Grumpy: great source of local freshly roasted beans;
• BÚÐIN NYC: check out the mod bar espresso machine-- pretty wild, plus you can buy some Nordic roasted beans if you're so inclined;
• Toby's Estate: the flatiron shop is connected to a Strand mini-shop and florist;
• Blue Bottle Coffee: they've expanded to Bryant Park but the Rockefeller Center location might be less hassle... if you can find it;
• Gimme Coffee: another good source of locally roasted beans.