Ok, so I'd actually recommend that on this first trip you stay in Tokyo as I think you'll have a LOT to see and do. Then on your next trip (because trust me, you'll want to go back immediately after leaving!) you visit some more places.
I would arrive, and do a good base hotel for Tokyo. We love the Shinagawa Prince Hotel. From there do all of the 'normal' Tokyo stuff, plus Tobu Zoo park and maybe LaQua, Yomiuriland, and Joypolis depending on your park likes. For 'normal' Tokyo stuff you should do the Ueno Zoo (Pandas!), Asakusa (shrine, good free viewing platform, tourist stuff), Shibuya (crossing, awesome food, shopping, etc.), Harajuku (interesting kawaii fashion and food), one tall building or tower, maybe the fish market if that interests you, take a cooking class from https://www.simplyoishii.com
, and just have an awesome time.
Then for your last few days and nights I would move over to a Tokyo Disney area hotel, we like the Hilton Tokyo Bay, and base there finishing off your trip before heading back to the airport.