I was just there in March.
I'm about 99% certain that the only place you can find Duffy and Shellie May is inside Tokyo Disney Sea. In fact, you can't even buy them outside of the American harbor area of the park (at least I don't think you can buy them anywhere else). There are two gift shops that sell Duffy stuff, and that's it.
Disneyland doesn't have them, and neither did the Bon Voyage gift shop near the train station (at least I don't remember seeing them there).
My daughter HAD to have Shellie May, so I went and spent way too much money on her, but my daughter is happy. Tokyo Disney Sea is beautiful and is worth seeing.
The trip from Tokyo is not bad (I went two days from Shinagawa and made the trip in about 40 minutes), and they have discounted tickets after 6:00 p.m.