B&H if you need diner fare east of Union Square (Matzo Brie, Best French Toast, Kasha w/ Eggs on Top (add hot sauce!).
Chelsea Gallery Diner if you happen to crave a spot west of Union Square - BEST BEST BEST pancakes - very flavorful for some reason (maybe they add vanilla in the batter). I have tried pancakes elsewhere all over NYC and still come back here!
Hmmmm. Off the top of my head, The Smith (I think they do breakfast), Friend of a Farmer, or 71 Irving? Maybe, The Adore.
I assume you mean on a weekday.
If you're willing to go deeper into the EV then you get more options like Cafe Mogador, Cafe Orlin, B&H Dairy, Stage Restaurant, Veselka, Caffe Emilia, Abraco (if you're OK with standing).