It's difficult to say what to compare!
- Size of the aquarium
Eight stories high building. As It says on the web page, it's one of the largest aquaria in Japan and possibly in the world.
One story and two underground floors. Easy to access from central Tokyo but smaller regarding size comparing to Kaiyukan.
- Fish tanks
Has many larger fish tanks comparing to Shinagawa Aquarium. In fact, they have very small number of small fish tanks and limits to display large tanks.
Normal size, normal fish. They have standard aquarium exhibition that most people imagine.
They focus on fish tanks and do not have performance stages such as dolphin performance. But they do have feeding performance in fish tanks.
They have a compact performance stage which feels very close to dolphins. The show is quite nice.
You can find out more about both aquariums from Hub Japan's articles.