In the past we have really liked...
The Breslin- in the Ace Hotel in Chelsea, they open at 7:00 AM for brunch on weekends, fun gastro-pub menu.
Locanda Verde in Tribeca also does both breakfast (8:00 AM) and brunch (10:00 AM) for Italian.
Maialino in the Gramarcy Park Hotel opens at 10:00, also Italian, yummy pastries and carbonara.