Universal is in Osaka, which, without a JRP is going to be expensive, especially if you're not doing any other travel outside of Tokyo.
Let's say you're staying in Tokyo for a tick, here's where i'd be at:
Go to Fuji-Q Highlands, it has a Thomas the tank engine land for the little ones and Japan's most craziest rides, period. I've written about it here: http://ourworlds.co/2017/reviews/fuji-q-highlands-review/
Get a 3 day pass to the Tokyo Disney resort, you won't regret it. Remember to commit though, Japan crowds are smart, organised and efficient, so if you're not there at 9am like they are you'll miss out on all the good fastpasses. Stay nearby - places like the MyStays Maihama are a nice joint nearby without spending a lot of cash. Above all else, go to DisneySea, it's the best park on the planet and it'll blow your mind.
Kawasemi and Regina are two fantastic Intamin coasters in one of the worst parks in the world for the simple reason they treat their animals like shit, and for as much as I just love Kawasemi, I can't recommend Tobu Zoo to folks.
O'daiba is a cool place to visit in the afternoon/evening and it's where you'll find Joypolis and a sweet indoor inverting spinning coaster that has joysticks on it so you can shoot things. It's just awesome. Plus there's new VR stuff nearby and an onsen "theme park" nearby you should try. It's like what Darling Harbour in Sydney should've been.
Head to Tokyo Dome and ride Thunder Dolphin. It's nearby heaps of other stuff so you can lump it in with other sight-seeing duties.
At this point you've spent roughly 5 days doing coasters and theme parks. If you have more time, then your stretch goals should be:
Go to Yimouriland, it's not filled with crazy amazing coasters but it's a fun day out.
Yokohama Cosmoworld is pretty cool too, plus the Kirin brewery is nearby and gives out free samples.
Hope this helps.