The best place to buy regional Kit Kats in Tokyo is at the Shokoku Gotochi Plaza. The shop is in the basement mall of Tokyo Station near the Tokyo Ramen Street, across the hallway from Rokurinsha ramen shop.
Kit Kat in Japan makes regional flavors that are usually only sold in that region. The Shokoku Gotochi Plaza features regional food items from throughout Japan, which is why the shop also sells these regional Kit Kats.
Some examples are wasabi, beni imo (purple sweet potato), azuki, mattcha, hōjicha (roasted green tea), strawberry, and more.
The Tokyo Station underground mall is huge. I get lost in there from time to time and I have a good sense of direction. The underground mall is divided into different sections and the Shokoku Gotochi Plaza is part of an area called “First Avenue Tokyo Station”, in Japanese, “Tokyo Eki Ichibangai”. Here is a map in English:
Shop hours are listed as 9 a.m. to 9 p.m., seven days a week.
Shokoku Gotochi Plaza