Often this is the brake rotors, and is pretty common. On my commute I was coming down from 8900 feet to 6700 feet in maybe 8 miles. Once I turned off overdrive to have the engine do part of the work, and spread out my braking so they had time to cool off, it would be mostly ok.
Many people say the Brembo rotors fix this, which you can get on Amazon among others. I ended up picking mine up at Auto Zone I think, getting generics. They were the same price as PepBoys and Oreily, but with a 2 year warranty instead of a 1 year.
But the 4runner (both my 98 and 92) have metal brake lines, so you have to disconnect the calipers instead of just moving them out of the way to remove the rotors. And that means you need to bleed the brakes. Because of this I've yet to do this, and may instead just go somewhere with my rotors and let them do it. It sounds like bleeding them isn't too difficult with 2 people, but it's an extra thing to learn and I don't normally have another willing participant.
Good luck. Looking at my records the rotors were replaced only 15-20k ago on my 98. There's many ways for them to get warped (overtightening, overheating), but with the hills and snow we have around here it was probably just overheating and then a splash of snow to quench them and warp them.
Aaron