I've been in Tokyo looking for some Studio Ghibli merchandise (Totoro etc), and found it hard to find a store selling the items. So to help others looking for a Studio Ghibli shop in Tokyo, here's the details you need:
There is a store called DONGURI GARDEN at one of the (many) shopping centres at Tokyo train station. The easiest way to get to it is going to the CENTRAL YAESU exit of Tokyo train station and then taking the escalator down. Almost immediately you should see a rank of shops that are selling "cutesy" merchandise from cartoons/anime/etc. One of these shops is called DONGURI GARDEN and it sells a limited amount of Ghibli merchandise, including Tottoro soft toys, Kiki's Delivery Service bags, Laputa stuff etc.
I will attach a couple of photos to this post once I get my camera working with my new laptop... having some troubles

OK here are the pics!
This is the shop:
This is the map of the relevant section of Tokyo station you need to find - just go down the escalator near the "You are Here" sign to the "Daimaru" shopping centre and you should see Donguri Garden almost straight away:
Good luck!