For thrill seekers, I would have to recommend Fuji-Q Highland (article). Many of the attractions here are ranked in the top ten globally in various categories (speed, spins, height, etc.).
It is a bit outside Tokyo, but can be reached within two hours by bus, train, or rental car fairly cheaply. Being at the base of Mount Fuji and the five lakes also gives you a chance to explore the most recognized area of Japan from up close.
I have been to several theme parks here in Japan and I have ranked them according to how I love them: (number 1, being the best)
1. Universal Studio Japan
2. Fuji- Q Highland
4. Disney Sea
5. Yokohama Cosmo World Amusement Park
6. Fuji Safari Park (If you will include this safari ride inside a grilled bus)
7. Niji no Sato (This are very few rides in here but I love the place)
8. Theme Park in Mie-ken (I forgot the name, though)
Other theme parks I heard that are good, but haven't been to:
- Nagashima Amusement Park in Mie Ken
- S-Pulse Plaza in Shizuoka City
- Grinpa in Shizuoka City
We go to Korakuen just because there is no admission charge and it's in the middle of the city. The LaQua roller coaster is quite a thrill and the flume ride is fine. The Power Ranger show is great for kids and fanatics. There's bowling, etc. Plenty of amusement park activities without the big committment up front.