Schiller's, on the Lower East Side, is a good steak and fries kind of restaurant, with a bar that serves excellent cocktails, and wifi. I've been in there with my laptop for extended periods of time in the less busy afternoon, and the staff were happy to let me sit. Rumor has it that they distribute donuts at 5.
Working from coffee shops is difficult in New York, as wifi is less common and less generously dispensed than in, say, SF. Think, near NYU, is, to my mind, one of the best coffee shops to actually get work done. It has consistent wifi (although it does cut you off after two hours), decent food, good coffee, and it's a large enough place that you don't feel self-conscious staying for awhile.
Marshall Stack is a great Lower East Side beer bar with wifi and a very cool bartender. I've frequently brought my laptop in and done work at one of the tables while drinking awesome Hitachino Nest Beer (which they have on tap and can serve you with appropriate sake pairings). They also have very good bar food that is served fairly late--I especially like the sloppy joe sliders.