I think the MO would be a pretty good choice -- the immediate surroundings are pretty uninteresting, but its building is directly connected underground to the Ginza Line, which gets you to many interesting touristy places in Tokyo in one shot, and it's close enough to walk to Tokyo Station if you don't have a lot of luggage.

The Hilton and Hyatt Regency are pretty far from the main Shinjuku station, but have separate subway stops right next to them which are somewhat handy.

Conrad might be a good choice since you would be fairly close to the Yamanote Line and have interesting locations within easy reach (Hamarikyu, Tsukiji, the train to Odaiba).

Besides those chains, you might also consider staying at Tokyo Dome City, which is next to a baseball stadium and amusement park, and has fairly decent rail and subway access to other parts of the city.