The Hampton Inn for sure.
That used to be this absolutely horrendous Howard Johnson - it was such an eyesore. I never thought that structure could be turned into anything without tearing it down but they proved me wrong. It has a really nice lobby, incredibly friendly and professional staff, decent complimentary breakfast, the rooms are larger than average, and the location is perfect.
The Hampton Inn is steps from the C and the E trains at 50th Street and a very short walk from a bunch more trains at 53rd Street / 7th Avenue, 49th Street / 7th Avenue, and 50th Street / Broadway.
You'll also be much closer to better and more economical dining options along Ninth Avenue where local people eat. Everything in the heart of Times Square is overpriced and mediocre (for the tourists).