We stayed at the Affinia 50 on an American Girl doll package. It is a very short walk up to the American Girl Place. You can walk it in 5 minutes. Very clean and nice. We had a two room junior suite. No restaurant though. Just a continental breakfast.
If you are looking for cheaper and out of the city. I can recommend the Courtyard Jersey City Newport Marriott. The PATH train is literally right next door. Take it right into the city. We stayed here for a Cheer competition that was help in the City and it was great. Clean, safe and relatively inexpensive.
Hotels that usually offer American Girl Packages :
HotelsAffinia 50
AKA Times Square
Grand Hyatt New York
InterContinental The Barclay New York
Marriott Courtyard Midtown East
Marriott Eastside
Marriott Marquis Times Square
The New York Palace
The Omni Berkshire Place
The Westin New York at Times Square
Peninsula New York
Sheraton Lincoln Harbor Hotel
Affinia Manhattan was lovely. Decent room; 2 queen-sized beds, kitchenette, nice service, directly across the street from Penn Station. It's on 7th Ave; I believe AGP is on 5th.