Children's Castle is still in business, and she might be just the right age to appreciate it. I'm guessing she might be a bit young for Kidzania, but they do have a whole range of activities, so maybe it's okay.
I'd also recommend the Toy Museum in Yotsuya - it's very hands-on and fun. Here are a few more ideas:
whereintokyo.com/dbinx/kids.html