My favorite breakfast in Manhattan is available at the Cupping Room in SoHo on West Broadway. My recommendation is off menu (I realized recently as I was giving a friend an extended culinary tour of the city that most of the time I order off-menu at most of my favorite places). This place has the best omelettes I've ever had anywhere in my life, and personally I always order one with cheddar cheese, mushrooms, and Nova Scotia salmon, a divine combination. It's this particular combination that's not on the menu, but they'll whip it right up. The place is a bit pricey, maybe $15 for a breakfast by the time you leave, but the atmosphere is classic and the food is well worth it, to say the least. Take the E train to Canal Street and stroll a bit north to find this jewel. A caveat: the place has two entrances with an "L" shape, so if you're meeting someone there, be careful that you don't wind up on separate sides each not knowing the other is there.