console it in if you are on the PC. Check the chest again, build up your alteration and learn the detect dead spell (Alteration 75) and try to locate the body. Pretty much your only options. I'm impressed by your looting choices though. Fifteen ancient nord axes, check. Seven iron swords, check. Mysterious Dragonstone...bah that's junk. heh
Uhm, those were actually my first thoughts as well. How can you just pass on a strange Dragonstone?
But, yea, you have to either find the Dragonstone ID and use the console or load an earlier save. I checked around the web, there are no other solutions. Some people say the stone is on a table, on the ground or in a chest. Just search the whole chamber. Although, I do remember finding the stone on the boss' body. Still, can't hurt to look for it around the room.