They were already a species inhabiting the wilderness in ancient times across many worlds, and even the sages do not remember their origins.
Unlike many D&D creatures, the bull-like gorgon was not invented from scratch by a writer, and as a result was not given a solid creation myth up front. Gary Gygax claimed to have taken the creature from a medieval bestiary.
The Ecology of the Gorgon (Dragon Magazine #97) describes Elminster's knowledge of the gorgon, whose petrifying breath even that archmage fears. It existed as a wild creature in Faerun at least as far back as Elminster's youth, c. 212 DR, where the people knew it by the name "stone bull". A gorgon once killed Elminster's dog.
According to that article, the information of which is attributed to an adventurer named Djaril Phylapur, gorgons hunt in pairs. This suggests that they may be naturally occurring magical beasts. They produce offspring naturally, so we know they can at least exist in the wild, although whether the original gorgon came from is evidently unknown even to the Sage of Shadowdale.
According to Ecology of the Chimera (Dragon #94), a gorgon can mate with a chimera to produce a sterile mule called the gorgimera. This suggests the possibility that the chimera and gorgon may be very distantly related. The chimera is speculated in that article to be a creature made by human experimentation, but it also says that the truth of that is lost to the mists of time. An argument against this theory is that the chimera can also interbreed in this manner with the hydra, which may more likely be a naturally occurring beast.
Elminster's Ecologies notes that the forest deities of Cormanthor have imbued the gorgons there with a curse that they turn to stone in water. This only says that the elven deities cursed that particular forest's gorgons, not that they created them; we might estimate that since those deities did not like the gorgon's design, at least those six gods did not create them originally.
The Petit Tarrasque and Other Monsters (Dragon #329) primarily describes the real-world origins of the bull-like gorgon and its likely confusion with the similar catoblepas, but gives this particular piece of in-world lore:
Both the catoblepas as described by Pliny and the bull-like "gorgon" are comparatively common throughout the known worlds and are discrete species. Such creatures would never be confused by anyone who witnessed both. The gorgon, therefore, does not appear to be an Earthly monster. Perhaps some plane-traveling medieval wizard is responsible for perpetuating this bizare name duplication.
This suggests, perhaps, that the gorgon was not, say, created by some wizard of a specific world, but rather it's a creature which has existed for a very long time across a great many separate worlds, and whose true origins have been lost to the mists of time.
The Ecology of the Catoblepas (Dragon #73) describes that even mages conflict over the exact nature of a "magical beast":
A magical creature, the wizards patiently explained, wouldn't need to breed, would it?
All right, retorted the naturalists, how come there are so many of them? Is some deranged thaumaturgist turning them out as an occupation?
The best information we have, then, is that the gorgon has existed in the wild for at least a thousand years, and if it was originally created by a wizard or deity, it was so long ago that practically nobody nowadays knows the truth.