If you want to eat traditional japanse food (kaiseki) ,you go to "koju" ginza.
It is expensive but delicios.
What kind of Japanese food would you like to eat?
There are luxury to popular things.
My recommendation is eel , soba, tempura bowls and so on.
You can eat it anywhere in Tokyo.
My area of recommendation is around Asakusa(near Skytree, Oshiage) or Ueno or Nihonbashi.
There are many old-authentic restaurants.
Thank you very much. I heard of this place where Anthony Bourdain visited and wonder if it is worth the trouble