After reading over the article provided, and doing a fair bit of reasearch on the topic, and, most importantly, the French Antiquarian Eugene Boban, I'm of the opinion that the skulls are fake. Various authorities have run testing on the artifiacts, including viewing it under an electron microscope, and they have shown that the skulls were made with modernized tools. Tool that the Aztec, Mayan, Mixtec, etc, could not have had access to. These cultures were using stone, wood, and possibly copper tools, not exactly easy to cut crystal (a very hard substance) with a piece of copper (a relatively soft metal).

I also perused wikipedia, since I find looking at the sources used to create their articles are usually reliable, and I found this, as a footnote citation in the article on the Crystal Skulls

As Philip Jenkins, former Distinguished Professor of History and Religious Studies and now an endowed Professor of Humanities at PSU notes, crystal skulls are among the more obvious of examples where the association with Native spirituality is a "historically recent" and "artificial" synthesis, "products of a generation of creative spiritual entrepreneurs" that do not "[represent] the practice of any historical community
Now, this leads me more than anything else to believe that these skulls are merely skillfully made fakes. In fact, I would go as far to say that Boban, the antiquarian manufactured most if not all of the larger, and therefore more noticed skulls. Take the following quote from NPR : National Public Radio : News & Analysis, World, US, Music & Arts
One thing the scientists have figured out is that the British Museum's skull came from Boban, that mysterious French collector. In the late 1800s, he first described it as a piece of artwork. Then he began calling it an Aztec artifact, in an attempt, Sax says, to make it "more appealing in order to sell it."
Note the word THEN. This means that it most likely wasn't an artifact to begin with, and therefore a fake. But there aren't any real ones, so it's just a made up artifact that was manufactured by a French Antiquarian, and bought up by Europeans and North Americans alike.

In conclusion, the crystal skulls were really an excellent business venture, and have evolved into senseless superstitions that appeal to others who believe that extra-terrestrials are real, or who believe in the Mayan doomsday theory.

Regards,
Steel


(By the way, thanks for the interesting discussion, I usually have fun researching things like this ^_^ )