You won't find a ton of breakfast places downtown outside of hotels which offer the insulting and near criminal $30 Manhattan hotel breakfast. You'll find your best breakfast on the street or in a Korean Deli where someone will break open a couple of eggs to make you an egg sandwich or omlette on the spot.
Downtown, you'll find a "coffee cart" at Liberty and Cedar right in front of the Chase Plaza. The operator has a smalle grill where he'll cook tow eggs with cheese and meat on a fresh kaiser roll for under $3.
At Cedar and Trinity Place you'll find a Korean Deli called "World" Sometyhing or another that will cook you up a fresh breakfast or breakfast sandwich on the spot for only a few bucks.
I prefer the coffee carts, because, in my opinion, New York street coffee is the greatest coffee in the world...for some reason.
If you insist on a fancy hotel breakfast or breakfast buffet the Drake (Swiss Hotel) in Midtown offers one that comes somewhat close to being worthwhile because it is partially uniquely Swiss in its offerings. Its refined, relaxed and the buffet is refreshed regularly. If my memory serves me correctly, it is $27 per person (thank god for the expense account).