Let me start by saying that I didn't go out to eat that much during my trip to Tokyo, but among the places I tried, GAYA was the best. The food was delicious. My partner and I shared four items, a trio of desserts and had some sake. Our bill came to around 9400 yen. The staff was very friendly, particularly the bartender, who chatted us up in English. We speak no Japanese, unfortunately, but we had a great conversation. You won't get full at this izakaya, unless you order quite a lot, but the flavors are outstanding. Definitely worth a visit. It wasn't very easy for us to find, but I think we had bad directions. It seems to be a bit of a hike from the nearest metro station.
Cons: Slightly pricey, Can be difficult to find