I have this same issue and surprisingly it is more pronounced after I serviced my vehicle at the dealer. Oil change and tire rotation and the 4runner never felt the same!
I went to the dealer and got the wheels aligned but still I get that feeling of driving a unibody rather than a body-on-frame vehicle which is why I bought the 4runner in the first place.
A long time back, I hit a really bad and wide pothole in a road. Saw it at the last minute and didn't want to slam the brakes for fear of getting rear ended. Loud thud and I think the right suspension might had bottomed out and hit the bump stop. But didn't notice any handling issues so I didn't bother to check.
Having said that, I am curious about how the sway bar works. Say if the right suspension is kaput, will the sway bar also transmit those vibrations to the left suspension? Considering that is the link between the left and right? Because the vibrations and rough ride isn't necessarily coming from the right suspension that I can feel or notice. So was curious.
Plus, I am still under warranty period for axles and such I think. I know its 36k miles for the suspension which I believe is just the strus and the coils. But will the warranty cover the rest?
I plan to take the wheels off and inspect the bushings and check for any play on the ball joints.
The suspension does dip like a boat so I am going to get the suspension upgraded anyways. Once I do that and the problem persists, then its off to the dealer for some diagnosis.Or maybe, wait to install the new struts after diagnosis as I don't want the dealer to blame the new suspension I put in.