It all depends on how much you want to spend. I used to work in Times Square and right across the street from our building there was the W Times Square. It was not cheap and I have heard the rooms are small, but the location can't be beat. Also, there is the Royaltan, which some people I knew stayed at when they came to NY for business. I think it is on 44th St btw 6th and 7th Ave.
The NY Hilton and Sheraton are all near Times Square and the Hilton Times Square on 42nd St btw Broadway and 8th Ave, near the the Port Authority Terminal. Again central location, though the rooms are a bit small.
bvamin