I feel your pain!!! I'm in the same boat. 63-72mph and I have a droning vibration. I have it in the shop right now and they still get the drone with the vehicle on the rack so it cannot be a suspension issue since there is no travel occurring. They have rebuilt the driveshaft, replaced the u-joints and are rebuilding the differential today. The bearing showed wear and a little slop so I'm hoping that by replacing them the drone will go away. Beyond that, I am at a loss.

 

I can only speak for my experience. I had bad vibration at 65 mph even after new tires, alignment and balance. It was still the same. My usual repair shop sent me to another repair shop that specialized in drive shaft issues. The other repair shop said my drive shaft U-joints were worn.
So they fixed the U-joints and removed and subbed out the drive shaft to a machine shop to re-balance the actual drive shaft. Total bill, $350 for everything. Went on a recent trip (12/2014) to San Antonio from Boston. The thing was so smooth and effortless at 80 mph.
Until then there had been a lot of vibration through the gear shift and from the back. I love older 4Runners and probably will not get rid of my 2001, ever!

 

I had the u-joints replaced, yokes replaced and the driveshaft completely rebalanced. Tires are 600 miles new and balanced. I haven't heard back yet from the shop as to if the rebuild of the rear end took care of the problem. I'm praying that it does.

 

Need some help, i've got a 2000 toyota tacoma 2wd sr5, replaced all 4 tires and rims, balanced 3 times, aligned, stock ride height, just replaced carrier bearing but truck is vibrating 45 mph and up, new upper ball joints and tie rods, cant figure it out

 

Check the steering rack. Turn all the way to one side. Grab the end of the rack that is sticking out and check for up/down play. Buy new, not rebuilt!
Check the u-joints. They might not show any play at all, so just replace them if you haven’t lately.
Transmission mount?
Wheel bearings?
I fought the same battle on my 4Runner...

 

Did you ever solve this issue once and for all ?