I commented on the Shinagawa hotels on your other thread. Here you talk about staying in Shinagawa and then getting out of the Shinagawa area for sightseeing on 8/9 and leaving your bags at Tokyo station. That defeats the whole purpose of staying in Shinagawa, imo.

Hotels offering discounts for JR Pass holders are the JR hotels. Info here:
http://www.jrhotelgroup.com/eng/