Here's the list I got in February. DD13 definitely will choose chocolate when it's available and I don't recall anywhere that we stopped saying they didn't have any. It also seemed as though in February it was the first time they carried Very Vanilla (purple) instead of the Vanilla (blue) everywhere.
MK: Main Street Bakery, The Lunching Pad, Sunshine Tree Terrace, Fryer's Nook
EP: Sunshine Seasons
AK: Restaurantosaurs, Pizzafari
DHS: ABC Commissary
Every resort we've ever stayed at has had Silk as well.
Not that you asked, but here's where they said we could get Tofutti ice cream (because every child wants ice cream).
MK: Plaze Ice Cream Parlor, The Cone Shop
EP: Fountain View, Sunshine Seasons (FYI: they've told us that they don't carry it but when I insisted that they look because Special Diets said they do, they generally find it)
AK: Dino Bites
DHS: Hollywood Scoops
ETA: I would definitely contact the Special Diets department to get the latest and greatest info. Things can and do change all the time. Last year we went to WDW in both June and August and I was shocked when a few products changed between the two trips. Contact info can be found in the stickies on the disABILITIES! board.