The Ioun Stone comes from Jack Vance's Dying Earth series, which is where the "fire and forget" spell casting of D&D came from too, as well as some of the spells such as prismatic spray. The stones are harvested from the core of neutron stars that are being sliced away by the Nothing at the edge of the universe and are therefore rare and difficult to obtain. Their origin is dealt with in the story "Morreion" in the collection Rhialto the Marvelous.
They were introduced in The Strategic Review, Vol. 1, No. 4, p. 10 (Winter 1975; no author given, although there is a reference to Vance approving the design/inclusion and I know he and Gygax corresponded) and first made their way into the rulebooks with the original DMG, as far as I can see.