BOG has the best cupcakes, IMO. Most others tend to be pretty perhaps, but absolutely covered in a mountain of highly dyed frosting- sad to say. One kids' cupcake at Narcoosee's was comical it was so gross. It was a Nemo cupcake. The kids - the KIDS - scraped off the frosting to eat it. There was an entire plate covered in bright blue goo! The frosting was so over-dyed, that it gave the frosting an unpleasant taste.
Also, WDW cupcakes aren't inexpensive!
Another one that was fun -ironically - was the paint-your-own cupcake. I think the last place I saw it was at the now closed Flying Fish. It comes with a cupcake, a white chocolate puzzle (sometimes), a paint brush, and an assortment of decorations and a palette of 'paints'. Once upon a time, they had it at Captain's Grille.
That said, WDW offers a fine array of assorted sweets!
Among the best are the signature dining locations. Sometimes, if you don't want to make an ADR/pay for a full meal- you can walk up on the late side- and get a table just for dessert and coffee.
I like the Main St Confectionary. I haven't been to it in a while, but the Candy Cauldron Bakery in what is now called Disney Springs was very cute! whenever we go, we HAVE to buy something.
Erin McKenna's Bakery NYC (formerly called Babycakes NYC) has delicious options, many (all?) are gluten-free! It is in the LANDING (what used to be called Pleasure Island area). They also cater to other food allergies.