We purchased single lollipops in our resort gift shop with snack credits. They are limited to the smaller sized ones not the really huge dinner plate-sized ones. They're usually all on the same rack so you have to look at the signage to figure out which are included and which aren't.
ETA: They usually have the racks of lollipops in each park as well. The Confectionary on Main Street, the large gift shop in AK by the tree of life, etc.