Stayed at the Le Meridien on a forced layover for a few nights. I thought it was a great location as it is in the Tokyo Bay area and was not crowded or congested and had beautiful views. Room was bigger than a shoebox and had a very nice bath with a window view of Tokyo Bay. Shopping is in the same area as well as the Hotel Nikko.
http://www.starwoodhotels.com/lemeridien/property/overview/index.html?propertyID=1838 http://www.hnt.co.jp/english/image_ex/access_map/access_map01L.jpg Or and the subway/skyway was right next door.
