Some more details please.
Did you disengage 4wd on or off pavement? Were you turning or going in a straight line? I disengaged off the pavement, and the clunk happened as I was turning to the left I believe
Where did the sound emanate from? Front or rear?
Sounded like right underneath my seat
What 4r do you have? Limited? SR5? What year?
SR5 2015
FYI, there is a TSB (technical service bulletin) about the rear propeller shaft making a clunking noise when 4hi was engaged (for 2010-2012 SR5's and trails):
http://www.toyota-4runner.org/5th-gen-t4rs/114053-toyota-issues-fix-axle-wrap-driveshaft-clunky-thumpy.html
I'm not saying this is the issue you are experiencing, but you should read the TSB and see if your own issues match up with what is described there.
There are other threads about similar issues:
http://www.toyota-4runner.org/5th-gen-t4rs/68916-axle-wrap-back-help-identifying-noise.html
http://www.toyota-4runner.org/5th-gen-t4rs/188133-clunk-when-going-4h-2h.html
Honestly, you're only going to get guesses from anyone on this forum, but at the very least if you provide details, others will have a better understanding of what it is you're experiencing.