I just had a new squeak start in my front suspension, after some looking around underneath the fj the only thing I could find was torn boots on the sway bar end links. Could this be the source of the problem or should I keep looking?
Sway bar links will make a clunking sound. You can tell they're becoming worn if you can move them side to side without putting effort into it. Most likely not the source of the sound you are looking for, but keep an eye on them because they're no longer sealed and will end up needing replaced.
If you hear it over a bump then it could be. Usually it's more of a metal on metal thud sound resulting from the wearing ball no longer fitting snugly in its socket and moving up or down quickly and hard making the sound you hear.