Do you have aftermarket wheels that have centercaps to cover the rear hubs? There are usually little lock tabs on the backside of them that seat on the hub so the centercap doesn't rattle around. If they get flattened out, the centercap can move enough to make an annoying clicking sound. I had this happen on a couple of different trucks. The way I found it was to put the rear up on jackstands and have someone else run the truck in gear and spin up the rear wheels while I listened from outside.
Cheers,
Sean