I've owned 2 4runners and a Taco all with the 3.4 (you didnt mention wether you were thinking 3.4 or 4.0) and towed with all of them (quads, dirt bikes and jet skis). While they did ok on the flat they always left something to be desired once the elevation started to change (heading over the pass). Don't get me wrong they did it, but it's not something I was comfortable with. Anyways, that's why I say get the V8. Of course larger brakes, tranny cooler etc. etc will also make a huge difference and should make the 4.0 more than adequate to tow dirt bikes and a light weight trailer.
Edit: My next purchase will either be a O5-06 Tundra or a v8 4Runner.
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Having owned a couple of 3.4's (2004 Taco and 1999 4runner) I can tell you that the 4.0 V6 is significantly more powerful. The 3.4's best feature is its reliability, not its power.
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Sounds like the OP is looking at 4th gens. Pros for the V8 are more power (obviously) and I think they might have a higher towing capacity, although I'm not sure about that since towing capacity is based on more than just how much power the engine puts out. The V8 4x4's also have full time 4wd which can either be a plus or a minus depending on how you look at it.
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I test drove both and chose the V6. It's been my tow vehicle for a 1,000lb teardrop for 3 summer seasons now (2012 - 2014) and it's worked great. There has never been a time when I wished I'd gotten the V8.
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MPG differences can be as low as 2 or as high as 10, depending on a number of factors including how "built" the vehicle is, and how it's driven. There are lots of guys over on T4R.org who are complaining about getting 13 MPG in their 4runners, both V6 and V8. Of course, they have 4" of lift, heavy armor all around, are running 33" MTs, have a full roof rack and are driven by twenty-something kids who mash the pedal to the floor at every startup, so you have to figure that's probably the reason for the lackluster MPG.
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The best MPG I've gotten out of my '07 V6 4x4 SR5 was about 23, but of course that was under "ideal" conditions. The overall average since I bought it in 2012 has been about 17.2 but that's skewed a bit low because I'd say 60% or more of that mileage is pulling a trailer (I have a separate DD that I drive to work and around town.) When not pulling the trailer I can get 18 - 19 average with probably 16-18 in the city and 19-20 on the highway. Of course, I'm not a fast or aggressive driver either, which helps (even when not towing, if I'm on the highway I'll usually set the CC at about 65 and let people go around me if they think that's too slow.)
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Other factors which may or may not be worthy of consideration: It's not unusual to see a V8 4runner for sale with 95,000 - 110,000 miles on it. That's because the V8 uses a timing belt and 100K is the belt change interval. That's roughly an $800 expense unless you can do it yourself. Many people would apparently rather sell than pay for the T-belt change. The V6 has a timing chain which does not need replacement.
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The V6 4x4 has a "multi-mode" 4wd system. You can run it in 2wd or 4wd even on the highway (basically, it is like an AWD vehicle.) Or you can lock the center differential and then it's like a conventional 4x4. Interestingly, this capability was deleted with the 5th gen models which only have conventional 4wd (which means you can't use 4wd on a dry paved road) except for the limited model which is full time 4wd like the 4th gen V8 models.
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Potential downsides for the V6 include some problems with the early V6 head gaskets. From what I've seen this is only an issue with the 2003 - 2004 models. I believe the VVT-I (Variable Valve Timing) version of the engine was introduced in 2005 and the HG problem seems to have been fixed as well, at least I don't recall seeing anyone having HG issues with the VVT-I engines. The '03- '04 V6's also have the 4 speed A340 automatic, which is less fuel efficient than the 5 speed auto that was put into the V6's starting in 2005 (The V8's always got the 5 speed.)
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Another thing to consider is that since the V6's have a 2wd capability, they have a vacuum actuated Automatic Disconnecting Differential (ADD) on the front axle. This can sometimes fail or need repairs. The V8's, being full time 4wd, don't have this, thus removing a potential failure point.
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You really can't go wrong either way, for me the V6 was the right answer but I know the V8 guys love their 4.7's.