I had both a 1st gen Tacoma (2004) and a 3rd gen 4runner (1999.) Both with the 3.4 V6.

Differences: The 4runner was generally more comfortable and better "appointed." It had better seats and more features like power windows/locks/remote keyless entry. The clock was actually visible on the 4runner whereas on the Taco it was annoyingly placed in a position where one of the "spokes" of the steering wheel covered it up, meaning that if I wanted to see what time it was I had to move my head over to the right to see around the wheel.

The 4runner felt "heavier" and I'm sure it was. The Taco would sometimes "skitter" around corners on low traction surfaces because there just wasn't very much weight on the back end.

In terms of driving, the Taco was a 5 speed manual and the 4runner had the 4 speed auto. The slushbox was terrible, worst feature of the 3rd gen IMO. For one thing, it killed both power (not great on the 3.4 anyway) and MPG (around town in Winter I typically got around 14 mpg in the 4runner where I was getting at least 16 - 17 in the Taco.) On the highway I only got over 20mpg a couple of times on the 4runner, but on the Taco I could do it easily (I once got 27 mpg on the Taco driving from Glenwood Springs, CO to Denver with my brother in the passenger seat and a full load of hunting gear. Obviously this was under super-ideal conditions but it shows what kind of MPG advantage you can get with a good manual transmission. Or maybe it just shows what a MPG-sucker an automatic can be.)

Overall I would say the 4runner was the "better" vehicle, all things considered. But the Taco was solid and reliable and had great ground clearance and off road ability even without the locker (the 4runner had the E-locker.)

My main reason for going from a Taco to a 4runner was that I needed to be able to carry passengers. If I was still single the Taco might have worked but as a guy with a family I needed something with usable back seats and a double cab taco was out of the question - those were going for literally double what I paid for my 4runner (which was under $8k.)

The used value of Tacomas (especially 1st gens) is, IMO, completely unreasonable and stupid but apparently there are dummies out there willing to pay top $$ for what is, by every objective measure, an inferior vehicle.

Still, I benefited from the high resale of Tacos when I sold mine, so I guess I can't complain.

Personally I would give the nod to the 4runner. There are some people who need a truck and for them I guess the Taco works but I think they're ridiculously overpriced for what you get.