There are several sweets shops in DisneySea (the Japanese are perennial gift-givers and packaged cakes and other sweets are always a favorite item to bring back home and hand out to friends and family), but the Merchant of Venice Confections is my favorite. It doesn't sell anything you won't find at other similar shops, but it is spacious and beautifully decorated and because it's separated somewhat from the main Mediterranean Harbor string of shops it's almost always less crowded. There are lots of places to find sweet treats to eat in the park, but if you want to bring some home I'd recommend a stop in the Merchant of Venice.
Even if you're not going to make a purchase, make sure to stop and get a picture of one of Mediterranean Harbor's best window decorations, Mickey and Minnie in a gondola being guided along by Goofy in the back of the boat. A static display, but very DisneySea.