Ender pearls aren't part of any "normal" organ. They're from the endermen's teleportation organ, which only endermen have. That's why you can use them to teleport. Given how much they hate water, I think it's somewhere in their feet.
(hey, if katydids can have ears in their knees, endermen can have ender pearls in their feet!)
I always thought they were ACTUAL pearls. I'll explain. So, when the Endermen travel into the the pocket dimension to teleport, they carry some unwanted foes with them. (such as the endermites) The endermites attack the insides of the Endermen and to protect themselves, they secrete an ender fluid around the pest forming a pearls. It gets the dark green colour from the ender-sick Endermen. Ender-sickness is caused due to staying in the end for prolonged periods of time and the ender dimension turns you black with obsidian which also explains the purple particles. This ender pearl theory also explains why the ender pearls have a chance to break and release the endermites which slowly returns to its original pocket-dimension.