Chris,If you want to walk to the spot for that classic shot with Fuji in the background, Chris Hood gives detailed directions in his article here...
http://www.hood-online.co.uk/publications/Fuji.pdf
He has also written other articles on how to get to other famous viewpoints.
http://www.hood-online.co.uk/publications/
In central Tokyo, views of the shinkansen winding through Shimbashi and Yurakucho can be quite artistic. Good vantage points are the Kotsukaikan Building roof (east side of Yurakucho station), the viewing gallery at top of the International Forum building (west side of Yurakucho station), and the observation floor at the top of the World Trade Center building next to Hamamatsucho station.