My '97 4Runner does it as well. I regrease the rear driveshaft fitting where it plunges and the clunk goes away for a few thousand miles. Quickie oil change places rarely grease the driveline, so if you don't do your own oil changes, it will probably clunk. I've had an auto trans '90 pickup that did the exact same thing. Grease it every time you change the oil and you will rarely ever have the problem again.

'89 Toy 4x4 Xtra Cab SR5 V6 266k miles
'01 Tacoma 4x4 Xtra Cab 2.7L
'97 Toy 4Runner Limited