if your pins and the check link is lubed and neither fix it do this.
your going to think i'm crazy for this but i have fixed many S/T trucks like this. when GM built the truck the hinges are lined up, after driving for a few years they some how become off line just a touch. open the drivers door all the way, now close it about an inch or two and then push it open really hard (not hard enough to make it touch the front fender though) and if you here a few pops than close the door and see if it still makes the noise.