To be really wise, pull a Carfax and have an independent inspection. I looked at one 4Runner that seemed like a good deal...until I looked at the Carfax and found that the last 3 owners each had it for less than 1 year. Warning flag!
Test drive, test drive, test drive. Not just around the block. Get the 4Runner out on the highway. Several low mileage 4Runners I looked at had a very noticeable shake/wander at highway speeds. It could be a tire/alignment issue, but it could also indicate serious suspension/steering issues.
Rear end sag is a known issue, though easy to fix, especially if you are planning on lifting it. A quick visual inspection will tell you if there are issues.
Check under the hood for a timing belt replacement sticker. This should be done about 90k, though an absence of a sticker does not mean it was not done. The 3.4l V6 is a non-interference motor, so if the timing belt fails, the risk of serious engine damage is low (unlike Hondas and others).
While you are under the hood, check the radiator fluid. It should be clear, not milky. There is a known issue with transmission fluid contamination (search "pink milkshake" on this site). Check for an external transmission cooler (should be in front of the a/c condenser).
About 2/3 of the 4Runners I looked at had radio antennae issues. Not a big deal, but if you hear a noise from the left front when you turn on/off the 4Runner and the antennae does not go up or down, that is likely it.
Put the 4Runner on a rack and look over the underside. Check for leaks, obvious damage, etc.
There is a site,
Toyota 4Runner History, that can give you some of the history, features, options, etc. for each year of 4Runner.