FWIW we were recently in Tokyo. You might consider at least a day trip to Tokyo Disney with a 6 year old. It will be the most non-tourist thing you do as it is about 99.9% locals or at least Asians. Rest of Tokyo is full of tourists. The Disney Sea park is really special and I am not a huge Disney guy. Lines are huge but really great place. Plus it's less than half the cost of Anaheim Disney. We stayed at the Sheraton Tokyo Bay which was very large but easy stop on the monorail, allowed more than 2 people in a room, had lovely club, and most incredible Japanese arcade. My kids liked the arcade almost as much as Disney.