Thank you so much everyone for all this wonderful advice! You'll make a 6 year old VERY happy!
I think the plarail may be our best bet. Will try Yodobashii and Toys r us Odaiba. Anyone know if the Akihabara Yodobashii also has a selection of toys? Or is Nishi-Shinjuku a better choice.
This trip will just be my sister and I - we won't have my nephew with us. But I will make a note of Omiya's JR museum for when we do eventually get him there!