There's no shortage of Western hotels on the Yamanote Line like the Conrad (near Shimbashi Station) all of the hotels near Tokyo Station (Courtyard, for example), and the cluster of hotels by Shinjuku. All will have front desk staff who speak English. I've stayed at some of the business hotels near Shiodome and Tokyo Station and they also had English-speaking staff. The stops on the Yamanote Line are all numbered and announcements on the train are made in English and Japanese (both by recorded voice and video monitors).