to be honest anywhere you go will be fantastic. I do recommend that you try the following Okonamyaki, Takoyagi and you must hit a Isakaya ( Japanese pub ). Its the common man's food & its great.
One of my favorite restaurant is Freddy's ( http://www.freddys-tokyo.com/ ). I go there when I need a little taste of home and Yuko the owner is fluent in English which is a great help.