We stayed at the Embassy Suites in the Financial District. It was GREAT!!!! We are a family of 5 and have a really hard time fitting in most NYC rooms, but not here. They had a wonderful, full hot breakfast each morning and a manager's reception each evening. This saved us LOTS of money, even if the hotel cost a bit more or was a bit farther out. Warning, however: it is very near Ground Zero and there were many people trying to sell books or postcards of 9/11 with pretty graphic photos. (not selling at the hotel, just in the area of Ground Zero) Our kids were younger and didn't know much about 9/11 and we really didn't want them to see all the images at that time. (This was about 2-3 yrs. ago, now they are older and understand more.) It is not as centrally located a hotel as those in Times Square, but there is a beautiful park nearby that overlooks the water and it is near the Staten Island Ferry. Taxis were easy to get and the subway was also close. It was a little more complicated as the subway stations around Ground Zero were closed, but we managed. I would stay here again.
Have a fun trip!