Just my 2 cents worth...

When I'm in Tokyo, I always end up at Sheraton Yokohama or Crowne Plaza Ikebukuro.

The reason being...the Narita Express stop at those stations (Yokohama and Ikebukuro). And when you've got luggage, it helps since the N'Ex does have luggage storage section in the Green cars. Then you just get off at the station drag your luggage next door to the hotel.

Both places have department stores next or close to them. Ikebukuro is on the Yamanote loop. Yokohama, on the other hand, is just a short ride to Tokyo Station, then the Yamanote Loop.

My personal favorite is Sheraton Yokohama. It even has a Citibank next to it for quick cash off the ATM if needed.

And no, I haven't taken the limousine buses yet since I always buy the JR Rail pass.