Dirty D.
Yelp
They have coffee, a variety of breakfast and lunch food offerings, and are open weekdays starting at 5 AM. It's not the best coffee but it's hot, fresh, cheap, full of caffeine and... did I mention they're the only place open at 5 AM anywhere within a mile? The chick who works there is sassy, the other two guys are pleasant and they remember faces and names pretty well. It's definitely a spot with a ton of regulars - general contractors, construction workers, taxi drivers, FedEx employees, beat cops and tour bus operators. They usually have the TV tuned to CNN and the radio blasting 80s hits while they sling their hash on the grill and chat up the customers waiting for their grub (no one should have to listen to Prince before they're fully awake, but I won't hold it against them).
As for the food, they have a shit ton of choices but I can only speak to one item, which is the only thing I ever get other than coffee - they make a DAMN good breakfast burrito! Steak or chicken, eggs, salsa, potatoes and cheese melted together in a flour tortilla with a 20 oz coffee will set you back $8 and change - a deal for the size and quality. I'm usually not hungry 'til noon after eating one...
The Deli Lama is a convenient early morning breakfast spot in a part of The City where there are few options. Check them out if you find yourself out in "Apparel City."
Tip: If you want to save some time and know what you want, call ahead - your food will be waiting for you in a to-go bag when you get there.