I too have a 1999 4runner (2wd though) and I'm having/had the exact same problem.
About a year and a half ago, my 4runner (@ appx 125k) suddenly started vibrating at the same speeds (50mph +). It seemed to pop up overnight and definitely had me worried. I worked down the street from a dealership, so I figured I'd play it safe and take it to them. That's where the circus began.
(1) they said I needed new tires, even though, to me, they looked as though they had another 10k left. I was also reluctant since the vibration came up so quickly, but they eventually talked me into it. Got the car back and no change.
(2) took it back in and they discovered the drive shaft was out of balance. They couldn't rebalance there so they took it over to another shop for the work.
(by the way, since I had invested in a set of new tires and their diagnosis was wrong, they covered this expense. One good thing about a dealer, when they're wrong they admit it.)
anyhow, got my car back and took it on the freeway. The vibration was better, but STILL there.
(3) back to toyota. Took, yet, another look and found that the shop that had performed the rebalancing had only rebalanced the front of the drive shaft AND NOT THE BACK! Luckily this time they gave me a rental since I didn't see my car for a over a week. They called me later and said they rebalanced the back, but the vibration was still there. They said I needed a new drive shaft because a seal around it had been worn through, causing metal to metal contact and it wouldn't properly balance. I was immediately suspicious that it had worn because of all the "out of balance driving" I had done between repairs. Nevertheless, this was an expense they won't cover. I gave them the OK just out of pure interest to get the problem fixed.
A day later, they called back. New drive shaft in and vibration still there. They dug even deeper. Now they told me that a bearing in the differential had gone bad and they would have to order specific tools to get it out. A week later they said the vibration was finally gone. I sat down in the car again and the vibration was greatly improved, but barely still there. Since I've been driving the car for so long and know how it drove before the vibration came about, I can feel it; even though it's subtle.
I moved around the time it was last at the dealership, so I haven't been able to take the car BACK in. Also, since it's so subtle and since I've already put a lot of money into the car to get it this far, I've just been dealing with the issue.
The only thing I can think of that may have caused the problem was when I drove 75 miles of icy roads with snow chains (no 4wd) several years ago. If you haven't driven on snow chains before, it's rough. Definitely rattles the car to death. The vibration may have thrown the drive shaft out of balance and consequently wore out the bearing in the differential. But who knows.
Anyhow, I hope this is somewhat helpful for you. I would definitely be interested in hearing what you discover. Especially since mine isn't completely fixed.
Sunday, June 22nd, 2008 AT 5:32 PM