To answer this, you need a perk, You receive this perk when you save "smiley the trapper" in the Kalamath, Just go back and talk with him after you save him and you get it, after that every gecko you kill, you'll get a pelt.
You have to finish the quest about smiley in Klamath. You go to the toxic caves and rescue him. Then he will teach you gecko skinning and some outdoor skill.
There is a mod out that allows you to skin the fire geckos as well. It is worth getting since the fire gecko pelts are worth 650 or so each.. Though they weigh something like 30 pounds each. Fire geckos are extremely overpowered though...
I wish there was a way you could have your pelts turned into armor at the tanner in Modoc, I have no freaking idea why that was not an option. Unless I missed something...