I know it's unfashionable, but my favorite place to stay in Tokyo is Ueno. Very accessible to Narita via the Keisei Railway station and to points north via the Tohoku Shinkansen. Asakusa, Kappabashi, Akihabara, Tsukiji, and Ginza are just a couple stops away via the Yamanote or the subway. For shopping, there's nearby Ameyayokocho and Okachimachi (guess I'm not the department store type). And for dining there are many izakaya and akachochin.