Quote from Phycozz
Creepers. And dungeons.
Dragon Egg is the rarest item not including sponges.
Rarest item not including the Dragon Egg would probably be the Nether Star.
Rarest naturally generated item would be the end portal frame, being only 36 per world.
EDIT: Actually, not including the Dragon Egg, I would say the End portal frame is the rarest item since you can theoretically get an infinite number of nether stars, but there's a limit of 36 frames.
I don't think the End Portal Frame counts as a resource, since it's impossible to mine.