They're likely alien skulls. Firstly, because that design is so organic that it could never be fashioned by human hands (it's hollow, even), and no human being has ever had a skull made from crystal. We also have an entire crystal skeleton, as noted by CHUD.com's reports and the product description for a figurine. Also, some other seemingly reliable reports have claimed that the skulls are in fact of alien origin.
Well, I'll say this: all the reliable reports (which even named Mutt before the name was officially released) have pointed to Mutt being Indy's son. And would "just another sidekick" really be getting all the focus that Mutt is getting?