We loved our meal in the SS Columbia, where we had a table overlooking Tokyo Bay.
In the Hotel Miracosta, in Oceano Restaurant, there is a very thorough breakfast buffet, which includes both western and Japanese breakfast items. It's a bit expensive ($30?), but a great place to load up on calories for the day. My wife would eat the eggs, sausage, fruit, pastries and yogurt, while I would load up on grilled salmon, rice and Japanese salads. DD could never eat enough yogurt, fruit, eggs, noodles, and pastries.
We didn't have a chance to try it, but the Bellavista Lounge in the Hotel Miracosta overlooks the mediteranian lagoon
*** I just realized all the above suggestions were for Tokyo Disney Sea, not Tokyo Disneyland. To be honest, we were not fans of the table service restaurants in Disneyland. There were excellent pastries in the bakery, the New York deli sandwiches were also good, as well as the Mickey Waffles (all counter service). But the sit down restaurants we ate in were just ok, but not worth recommending. Sorry.