Just did an oil change on my 99 SR5. While underneath, I noticed both outboard CV boots have started to puke milky grease.
So the question is do I repair or replace them. I'd prefer to go the replacement route, but my experience with other makes has taught me some aftermarket shafts are junk.
Are aftermarket axles for the 4Runner any good? If so, which are the most reputable?

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Buy a reman from NAPA, at least it will be mostly OEM. All new are Chinese. NAPA does offer a long travel new axle for lifted vehicles for about double the money of a regular one.

It all depends who turns in their oem's as core. In my experience not too many.

In my location I went to various auto parts stores, Napa, Orielly, Advance, etc.
They all have rebuilt oem shafts in they're illustrations. So I ask the counter guy to pull at least 4 shafts looking for a rebuilt oem one. Couldn't find any.

I got 2 sets of oem boots and I'm just going to reboot 2 oem shafts I found at the yard. Keep them as ready to go spares.

I wonder if the Toyota remans are more reliably OEM than the referred to Napa ones?

If you have OEM CV axles, just reboot those. Aftermarket CV's are weak and also unbalanced, hence pulsations and vibrations at high speeds.

It's easy to replace CV boots. No need to remove the CV axle from the hub or from the diff.
1) Remove upper or lower ball joint (no need to remove LCA: I was installing bushings at the same time)
2) remove the clamp on inner and outer CV boots
3) Pull the boot off the inner joint
4) Remove C-clip and pull the tripod bearing
5) Remove both inner and outer CV boots off the shaft.
6) Slide the new outer boot on to the shaft, pack grease and install clamps
7) Slide the new inner boot and then tripod bearing, install the C-clip, pack with grease and install clamps.
8) Install the tripod bearing into inner joint and install clamps

That's it. I did it about a month ago and it was super easy.

Buy OEM boots Toyota BOOT KIT FR DRIVE 04438-35062 : Same part number for both sides: Each kit comes with clamps, grease and two boots per side

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dont you need a special tool for the clamps ?

An Oetiker style clamp pliers is all that’s needed. Irrigation places and probably Home Depot carry them, as well as Amazon I’m sure.

I have about 1000 miles on the Napa “lifted applications” set of CVs. The boots don’t seem to rub it all with a 2 inch suspension lift on 265/75s.

Napa part number is 94–1258. You’ll need to reuse your old CV nut though as the one that Napa ships with it does not fit the Toyota keeper well.

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That's slick!

I was thinking of ditching the inner oem boot for the CVJ's BOOT 68 higher angle boot. I've read some members did this.
The whole CVJ's rebult axles are good too.

Boot clamp tool: Lisle 30800

You need thos tool only to tighten the larger clamps on inner and outer. the smaller clamp just require a plier and a hammer to bend tabs.

DO NOT BUY CHINESE cheap tool. Mine broke in the first attempt.

Before you crimp, make sure the entire clamp is on the boot. It could slide off the boot if it is not properly in it's grove on the boot (happened to me and cannot be stretched once crimped!) . You can also use metal cable ties available at NAPA.

Replace. Rebuild the original one and keep as a trail spare. It's a good exercise too to know how to rebuild one just in case you need to do that on the trail.