3 days in tokyo itinerary

My 7yo daughter's dream comes true! She, my 4yo son and I will be traveling to Tokyo from Beijing in a few weeks.

Here's my plan:

Friday: Arrive Narita at 2 pm
Check in at Keio Plaza
Check out Tokyo from the Tokyo Metropolitan Gov. Offices
Play at Shinjuku Chuo-Koen for a little while then have dinner and early to bed

Saturday:
Trip to Yusunne in Hakone for amusement spa park

Sunday
Ghibli Museum in the morning, walk through Inokashira Park and visit Temple of Benzaiten
Afternoon - check out the harajuku girls at Meiji-jingu and adjacent sights

Monday
Disney Sea - we're from LA, so Disneyland is old hat for us - fly back to Beijing in the evening

Any suggestions?

Looks like a perfect plan to me, except that the day at Disney Sea will be a little bit short, because I recommend to leave Disney Sea about 5 hours before the departure of your flight just to be safe.

5 hours, really! I figured 3 would be enough. Since we're going for such a short time and I'm a light packer, I was only planning on bringing a backpack. That way we don't have to return to the hotel before going to the airport. It looks to me like the a bus directly to the airport will take approx. 65 minutes. What will we do at the airport for 4 hours? Do they have a play area?

Jackie