I assume if you are going to Hakone, you will be staying at a Ryokan. Most Ryokans at a certain price level will have pretty good kaiseki dinners served in room.
There are also many great kaiseki restaurants in Kyoto as well as Ryokans that serve kaiseki in Kyoto. There are also many kappo restaurants (kaiseki style food served over the counter as opposed to in a private room).
I heard Tsukiji will no longer be open topublic at some point and also you have some super long lines for some of the restaurants inside like Sushi Dai.
Here is a very reputable source for Japanese fine dining though it contains posts for elsewhere too
http://www.luxeat.com/reviews/by-location/tokyo/
If you can navigate tabelog, you can sort by rating for the type of cuisine you want. Also, while Jiro might not be the "best" compared to the very tip top of Tabelog, its still going to blow away everything outside Japan and 99% of places within Japan.
Also, dont miss out on western food. The French fine dining, Italian fine dining, patisserie, bakery, chocolates in Japan are every bit as good as Europe.
Last edited by amoeba; 04-27-2017 at 12:28 AM.