Owned all three iterations - 3rd Gen 4Runner, 1st Gen 4-door (DC) Tacoma, and ext. cab Tacoma (1st Gen). First, I will say they are ALL great vehicles. I did not have any problems with any of them. Here are my thoughts:
4Runner - Great interior space. Short wheelbase (pro or con, depending on your use). Coil springs all around. If you need 4 doors and would like to be able to access your gear from the inside of your rig, it's hard to beat a 4Runner. The negative for me was no truck bed.

But you could get a trailer for "truck bed" projects. Also, I don't know if this was in my head, but I felt my two 4Runners all rode worse on washboard/fire roads than my longer wheelbased Tacomas. Felt a little bit less stable as well. But that could be a number of things, so again, probably just in my head.
DC Tacoma - 4 door was great, although I believe the back seat is a little smaller than the 4Runner. Still, no problems for me or passengers, or with a baby seat. Even though it was made in the US (vs. Japan for all 4Runners), no quality issues, except dash rattle. Rear leafs were ok, though I'm sure some Alcans or Deavers would've made a big difference. Reason I got this was for the truck bed. It is SO nice to be able to just toss all the dirty, dusty, grimy, wet, muddy, smelly, filthy stuff in the back without having to smell it or stuff it in plastic sacks. Plus, I had a pipe break and had to redo some drywall. If I had to haul sheet rock in the back of the Runner, it wouldn't have been pretty. Oh, then there is the spring-time mulch, manure projects. The price is high, but so is the resale value. It will sell for more and quicker than a 4Runner, and will hold its value for longer as well.
Ext Cab Tacoma - I only got this truck, because I've already got a capable 4-door SUV (UZJ100). This will be for solo outings or +1. I was without a truck for a while, and began to miss the utility of a truck bed. The rear space is not fit for any normal adult and even a scrunch for kids. I just use it for cargo. The manual transmission is also very nice.
What it comes down to is, do you need a truck bed? If not, go with a 4Runner. It is one of the best expedition trucks produced. Even in stock trim, you will be able to get through some crazy trails. For ME, I cannot do without a bed (or don't want to). If I'm forced to have just one truck, I'd get a DC Taco.