Seki
http://r.gnavi.co.jp/fl/en/g194800/
Reservation advisable.
Counter seating = Yes
Credit cards = Visa / DC
This restaurant is in the most atmospheric, narrow, cobble-stone alley that I know in Tokyo. Even if the food weren't great it would be worth visiting for the scenery... but the food is great and reasonably priced with kaiseki options from 6,000yen. (My bill is usually around 10,000per person at the end of the evening).
Print a copy of the menu from the above website, because the one in the restaurant is illegible ... even to Japanese people.
Print a copy of the map from the above website because the restaurant is impossible to find without one ... even for locals. (Hint: Walk up Kagurazaka to the gaudy temple. On the other side of the road is a narrow alley with a sign for "Le Bretagne" ... walk down the alley, past "Le Bretagne" and turn the corner... Seki is on your right).
Seating - Be sure to ask for a "counter" seat when you make your reservation. This will allow you to occupy one of the "park bench" type seats at the counter.
The website claims "English spoken" because the "master" lived in Ealing (London) for a while. The welcome is incredibly warmm, but let's just say that his English is ... interesting.
The 90 year-old Grandmother will bring you the bill at the end of your meal and will follow you out of the restaurant repeating "Thank you. Please come again. Thank you. Please come again. Thank you... "
Guaranteed good time.