Our "go-to" toy store in Tokyo is called Kiddyland, located in Harajuku. The last time we visited, it was in temporary space while awaiting its new premises to be completed nearby. They could be moved into their new location by now for all I know.
Both toy stores that I have visited in Japan have left me a bit underwhelmed (the other is Hakuhinkan in Ginza). And they are nothing like, say, a Toys R Us in the U.S., with their unlimited selection. That said, their inventory does consist of uniquely Japanese products that are by and large unavailable in the West.
However, if your nephew is anything like my son, he probably has everything he wants already (!) so I would visit him first, check out his existing inventory, then go out shopping and make a purchase.