There is a fine dining restaurant at Tokyo DisneySea. It is called Magellan's (after the explorer of course), located in the Mediterranean Harbor section of the park. From the outside, it seems like any other restaurant, but once you step in and look it become quickly apparent that is it not the usual Disney park dining options.
It is decorated like a club for Age of Exploration explorers with a few light Disney touches. The waitstaff are wearing costumes, and it is a well decorated and impressive space. We sat under the huge spinning globe which was awesome. This is themed dining combined with fine dining without going overboard and you get to enjoy it without being stuffy.
You should get a reservation ahead of time or go outside of the usual meal times. Very much worth it.
We had the Pacific course which had a choice of starters, soup, entree, dessert and coffee and tea.
There was an option to get the souvenir Frozen Queen Elsa Coronation fork and spoon set with the meal as well.
If you are visiting Tokyo DisneySea, definitely eat here once. For in park restaurants, it is second only to Monsieur Paul at EPCOT and tied with Tiffins at Animal Kingdom.