JJF: The lack of proximity to Hombu isn't a huge problem - we lived in Toronto for several years, so we're used to taking transit everywhere (though I imagine the system in Tokyo is just a bit more complicated...and crowded
). I'll definitely check out Minato-san's ryokan!
When you compare Toronto to Tokyo, so Toronto is like small country town. In Tokyo they have I think 25 lines of subway...and additionally everybody walks left side of the sidewalk ...
Bon voyage and enjoy your vacations.