Hi, and welcome to the forum.
I think your problem has to do with the shock/spring (strut) assembly.
There are three possible causes:
1. Insufficient clamping force of the lower control arms to the subframe (sharp metallic pop when accelerating or decelerating)
2. Front shock spring coil contacting the end of the spring (clunk when driving over dips)
3. Bad front shock (thump over rough roads)
Either way, get Toyota to look at it. I think this problem is not uncommon in the new 4runner (more common in 4runners with XREAS??). I believe Toyota will replace the front struts for you or retorque the lower arm mounting bolts...depending on which problem you have.
Hope this helps...and good luck!
(BTW, i could be wrong on all of them...so take my word with a grain of salt.)