The best two aquariums I’ve been to in Japan are the Kaiyukan in Osaka and one in Okinawa. Not sure which I’d say is best, but the Osaka aquarium is very cool.
You start by taking a long escalator ride to the top of the building. The general layout is a giant central aquarium with a walkway winding around it. Making its way around several times before reaching the bottom. The central aquarium represents the Pacific Ocean and increasing depths reveal different kinds of fish. Probably the main attractions are the Whale Sharks and Stingrays. As you make your way around, looking outward from the central tank you’ll find many other fish and animals presented.
It is a well spent afternoon. Next door is the Tempozan Marketplace, mall with all varieties of food…and Legos.