Do you want drip coffee, straight up espresso, or a fancier espresso-based drink? Are you looking for croissants, scones, donuts, other pastries for breakfast to-go? Or other, heartier fare with sit-down service?
Here is my in progress list of great brunches in NY:
Here's a list of breakfast places that serve deliciousness on weekdays (lots of NYC restaurants don't):
+ add onto that list Cookshop, Square Meal (I think), Egg, Landmarc, Shopsins, Community Food and Juice, ino.