I tried to crank mine a bit tighter too but it still rocks like a babies cradle.

 

try loosening it a little and shifting it front or back and then retighten it. it could just be off-kilter or something.

 

StingRay, is your winch crank thingie rusted up? Can you lower the spare? It needs to be cranked up to the frame to not swing around. Use some penetrating oil on it for a day or two and try to break the rust out of the crank.

 

This Runner only has 60 thou hiway miles on it and is super clean. The winch is free and smooth. The tire is cranked tight enough to leave indentations in the tire where it rests on the cross member and the pads and is as far back as it can go. I checked others on the lot and they rocked exactly like mine, the newer ones did not. I actually got under a 2002 that was on a display rack and noted the new front pads and the emissions can above the tire. The tire on the new one is also tilted down lower at the front.

I actually work as an Engineering Technologist for an RV manufacturer and design/prototype underbody bracketry as a major part of my job and this tire rocking/clunking bugs the HECK out of me. I am going to make some front pads like the later gen 3 runners have. I am a long time Toyota man. My wife and I currently have 3 MK2 Supras and between us this is our 9th Toyota but only my first truck. I am amazed at the lack of attention Toyota gave this spare tire holder.

Thanks for all of the responses and the warm welcome.

 

you can always just fold some cardboard and jam it between the tire body or a couple of match books or something.

 

Ya sure I want to see that 3" matchbook it's gonna take to fit between the tire and the floor cross member or the entire cardboard box that's it going to take to fold up into a thick enough shim. Maybe I should just jamb a 2X4 in there and nail it to the tire so it doen't fall out.

 

I once had a shock bushing rot off the passenger side stem and I grabbed some cardboard to make a quicky bushing to get home with out the thing banging on every bump. hehe.

 

I have a 2000T4R and this noise has been driving me crazy.
My 2 kids make a game out of it when they sit in the back. Who can find the location of the sound?
I removed all the panels and the rear carpet. bounced on the bumper with no noise. Hit the roof and sides of the rig with no noise. I tried to find all the loose items wires drains and things like that behind the panels and under the rig. I tried shaking and shipping the roof rack with no noise. I found there is a drain tube on the passenger side that comes from possibly the sunroof and drains behind the rear tire. The tube is about a 1/2 inch and lays on the inner wheel well it was flopping around and sounded similar to what I heard. I was able to pull the slack out of it and tuck it in the V section by the inner wall and wheel well. I am hoping this was the issue as I don't know what else could be making the noise. I have gone through all the suggestions and this was all I could find that would make noise.
Fingers crossed. I will update once I hit some bumpy roads.