Hi,
Agree with Haley on Team Borderless Lab in Odaiba, make sure you do the drawings as it comes to life

! Also, if anyone is a big Gundam fan, they do have the huge Unicorn Gundam Statue by the mall there as well to take pictures with.
We also went up the Tokyo Sky Tree, similar to the feel of the Paris Eiffel Tower experience but everything was inside. They do have a glass floor to allow you to look down.
We rode the Shinkansen to Nagano from Tokyo Station and it was a great experience. I actually had a kick watching the workers clean it and how they acknowledge when they're done as they lined up outside and bowed before we got on, not sure if they do that regularly.
If you get to Yokohama ( i know it's not in your itinerary ) def need to check the Cup Noodle Museum, it was fun for the family, we got to make our own ramen noodles there (and was cheap to do)
We stayed primarily by Disney so we took the Limo bus to and from Narita. Was pretty easy and straight forward,similar to how Disney World works from Orlando and the bus schedule. We purchased one way from the airport to the Sheraton and at the bell desk at the Sheraton a few days before. The buses were comfortable.
Have a great time, you're going to have a lot of fun!