The really good restaurants, even small joints, are full all the time, even without tourists. So, if you want a really excellent meal, be prepared to wait, or find a place where you can make reservations. :-)
Like the OP I was also in Japan this momth for the third time (first time in 2017), visited 4 major cities and few more towns.
Never ever had I book a restaurant to eat good good. Yes, there were places that were packed but there was even more places that weren't and still had excellent food.
It's just being spoiled and going after google maps reviews/ratings at this point and not really enjoying the place.