I had my truck in about 2 weeks ago and they replaced both rear shocks. I would have sworn it was coming from the front as well, but replacing the rears seems to have fixed my clunk completely. It feels like such a better truck. I can't believe I had to wait over a year and 25,000 miles before my Raptor rides like it's supposed to.
I did have to find a different dealership than I purchased the vehicle from before I could get anythingat all done. Heritage Ford in Modesto, CA was absolutely worthless for me on everything I asked them to look at and told me multiple times that it was all normal and I was wasting their time by complaining about it, not just shocks, everything. Terrible dealership experience. Price Ford in Turlock, CA has been close to excellent getting these shocks replaced and a few other issues I've had pop up.
Now if they can fix my exhaust rattle I might be happy.