Definitely Ghirardelli Soda Fountain and Chocolate Shop at the Marketplace in Downtown Disney. I also really liked the hot chocolate at Kona Island Cafe Coffee Bar at the Polynesian.
We were at Disney for my brother's birthday once, and I distinctly remember my mom handing me a cup of Hot Cocoa from the All-Star Movies food court before we spent the day at Downtown Disney. It was the best cocoa ever, it even had whipped cream!