There are so many unique Tokyo Disney souvenirs, you won't have any problems finding them in any store! From the different plush characters they have, the extensive range of stationery and phone and bag charms, the Nanoblocks, all the food gifts...your mind will boggle with choice!
if you're going soon, there is also the Happiness range (for the 30 year anniversary), and merchandise for new year, both thr Japanese and Chinese version (Mickey's dressed in horse costumes and lots of Bullseye stuff for the year of the horse).
If you're looking for homewares, there is a Home store near the entrance of both TDS and TDL. I found the one at TDL particularly good. A tip for any shopping, if you can spare the time, go before the afternoon. They get very busy at that point! Going early will give you time and space to really look around.
One store I really loved, and is pretty obscure, is the Disney Gallery in TDL. It has a small entrance of just a set of stairs. Up there you'll find a small exhibition of artwork along with some really special figurines and books, etc.
Oh, and if you want something with Tokyo on it, there is also the crystal store near Cinderella's castle. They have lots of figurines on stands saying Tokyo Disney Resort.
Have fun shopping!