After trying to swap out aftermarket pads and rotors on my last car, 95' LS400, I gave up and replaced everything with OEM. I kept running into squeeks, groaning noise, clicking of pads, wobblie hop due to rotors not centerable, etc... Spent probably 3x's of what it would of cost me just to order new oem stuff from one of the online venders off of
www.parts.com. The thing to remember is the shim kits and fitment kits. Many aftermarket pads are just pads, that slide into the calipers. I haven't tackled the brakes yet on my 4runner, so I have no idea what's in there, but judging by other Toyota products, I'm willing to bet there are shim kits that attach to the back of the pads to prevent squeeks, groans, clicking "pads shifting around in the caliper", etc...
With that said, my opinion is oem. But, again, I'm bit of a newbie with the 4runner, and haven't gotten to the brakes yet...but soon, as they're needing some attention these days.