City - 5 aquariums (metro area)
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Where are the best places to marvel at manta rays and hang out with penguins? A lot depends on how much time you can spare, but while the biggest and best spots may be well outside central Tokyo, there are some respectable options right in town. Here they all are:

5. Viewing tunnel and "Jellyfish Ramble" at Maxell Aqua Park (Shinagawa)

Crowd-pleasing attractions at this recently renovated aquarium include a walk-through viewing tunnel and a relaxing "Jellyfish Ramble" where you can wander around a forest of illuminated jellyfish tanks in a dimly lit hall. Very splashy, well-choreographed dolphin shows are another draw.
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maxell
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4. Sunfish and sea lion shows at Sunshine Aquarium (Ikebukuro)

Conveniently located in an urban shopping mall nowhere near a body of water, Sunshine Aquarium is most famous for its huge sunfish and manta rays. There's also a big colony of penguins, and a popular sea lion show that's held several times a day.
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sunshine
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3 Tuna tank and petting pool at Tokyo Sea Life Park (Edogawa-ku)

The most beautifully designed facility on our list, Sea Life Park is built around a massive doughnut-shaped tank where schools of tuna swim around in circles. The gift shop also stocks the most tuna plush toys we've ever seen in one place.

Resident sea birds include puffins, auks and of course penguins - one of the largest colonies in Japan. There's also a petting area where you can touch starfish, bamboo sharks and sting rays.

[Note: while this has the cheapest admission fee on our list, unlike other aquariums there aren't any animal shows to see, so it's more of a one-hour diversion rather than a half-day's entertainment.]
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sealife
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2. Trained-fish and jellyfish shows at Enoshima Aquarium (Fujisawa)

A large and biologically diverse aquarium, Enoshima is probably most notable for their world-class jellyfish collection. Who could possibly resist a visit to "Jellyfish Fantasy Hall" to take in their multimedia "jellyfish show with lights and sounds"!

There are also numerous dolphin, sea lion, penguin and trained-fish shows, and interactive programs where you can feed sea turtles and shake hands with dolphins for a small additional fee.
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1. Interactive zone and giant sea turtles at Yokohama Hakkeijima Sea Paradise (Yokohama)

In terms of sheer size, diversity of attractions and overall number of resident animals (over 100,000), Hakkeijima Sea Paradise is the clear leader.

One draw for families with kids is the big interactive zone, where visitors can get up close to the dolphins and pet the sea lions, and children can take off their shoes and splash around in ponds full of fish. The three-story main aquarium complex is home to numerous penguins, sea otters, some very large crabs, and giant sea turtles.
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hakkeijima
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