NE1 familar with 4runner suspension?
 

I have the 99 Toyota 4wd 4 runner and anytime I get the car over 55mph, it's starts swaying back and forth like crazy.

It had a differential problem, and the guy redid the bearings in the diff. Not sure how good of a job he did. I'm also sure it started to happen after the diff change, but am not sure if the two are related.

Any suggestions as what to check?

check your sway bar end links.

Like when you have a trailer without enough tongue weight?

I dont know how that feels. It sway like being on a boat (left to rt) but alot faster

It's not just wind buffeting from other vehicles around you? It's a pretty tall vehicle, and catches a lot of turbulence from big trucks and passing cars.

Maybe the diff could be at fault. It sends power to one side, kicking that side up a little, putting more load on the opposite side, which in returns kicks that side up a bit, and it feeds off itself and creates a rocking motion? I'm not a diff guy, and have no idea really, but I would imagine having the spacing set up incorrectly could maybe cause something like this.

Well I have a 4runner but it's an 85 with leaf springs and two solid axles, so not quite the same as yours LOL.

Does this swaying manifest itself in the steering system at all, such as wandering L-R down the road (ball joints or tie rod ends) or is it just the body swaying? Sway bar problem? Blown shock perhaps? Does the swaying happen at a consistent rhythmic pace or it is kind of random?

Good places to ask/search for 4runner-specific info would be yotatech (many later model yotas) and 4x4wire (fewer late and more older yotas) or if you want a more mt.net-style experience where dumb noobs get the shit flamed out of them for not searching through all the good tech info, try pirate4x4.

Its ver consistent and rhythmic. it is not felt in the steering wheel either., just felt in the body. Definitely not the wind knocking the car around.

can alignment cause this?

So it's "tail wagging"? That would be what I was referring to with the trailer reference.

Alignment issues would most likely pull you to one side vs swaying unless this is some sort of lsd then you could be getting what has been suggested in the diff occasionally compensating. Though a diff doing that wouldn't likely be a strongly felt effect IMO, certainly not as strong as the wind of a semi passing you.

I'd go under the thing and check bushings, joints etc to eliminate them. Look at the rear tires, do they look like they have wonky toe?

Is this all coming up right after the diff repair could it be reinstallation error? Ask the guy who did the work what gives?