Honestly, I would call the cold stone manager tomorrow and discuss this. Personally I would have stood there and gotten my ice cream--there was actually no need to treat you like a perv. If I was the manager at Cold Stone, I would have looked at the age of the child and known that kids say the darndest things... and let it go.
As a parent/teacher, I see kids all the time. When I sub in the Pre K preschool classes, I have three year olds. They are supposed to be potty trained but they aren't sometimes. Professionally I won't touch *****hes, but I have been known to zipper/pull up pants. At 3, your nephew should be doing it for himself.
This could be a lesson for him to learn to do it himself.