I've never done either one on a 4runner, but I've lots of experience with turbocharged cars AND supercharged trucks.
I am curious why, not including costs, you feel turbocharging is better. Mostly because I've found non-diesel turbo vehicles don't have the torque curve I would want in a truck. I drove 1st gen Toyota's with the factory turbo and they were anemic. I'm not saying yours is, that was just my experience 25 yrs ago. Superchargers can be geared for power right now, turbos have to wait for the spooling. I know that is a general statement, not speaking from 3rd gen experience. I just find the topic intriguing, and always enjoy getting first hand knowledge.
Reasonable question to ask, my opinion is based on the following...
Yes, my turbo truck is very anemic, but it's not the turbos fault if it's mounted to a 30 year old 8-valve/low compression truck motor.
OP never mentioned he was intending to wheel with the boosted setup until the last post he made, the supercharger is probably the better choice for the immediate torque curve. Heard a lot of good about these roots types and torque. I feel it with my butt dyno.
My personal reasoning was cost, but if you rule that out, my other reasons include potential power and versatility. I don't mind turbo lag, but obviously that is completely dependent on turbo size and usually miniscule with low boost and/or smaller turbo applications... yadda yadda.
Online, there seem to be several people who run turbo 3RZ's... even on stock bottom ends. At that point you could just run more PSI with the turbo than the supercharger is capable (IE: 12 or 15 PSI). 300+hp/tq on a stock bottom end is impressive for a 4 banger that makes 150hp/180tq stock. Then again, I'm not rock crawling with my truck all the time, I use it to commute while wheeling trips only happen every now and then. I don't recall ever having to use boost out on the trail, especially with low range. Usually idle or a little gas is more than enough for my type of wheeling.
The supercharger in question is the Eaton M62 blower, a very small unit... I've spoken with the fellas over at Magnuson Superchargers and they say that 10 PSI is typically the maximum, they recommend no more than 8 PSI. Running 10 PSI plus meth is probably the best option for getting the most from the S/C. I've have yet to run more boost on my S/C but I'm sure I will want more when it's all tapped out. Other qualms include the lack of intercooling after the superheating of air, it is harder to control between the blower unit and plenum (Maybe 6-8 inches between the blower and head? No room for an intercooler). The meth could be a good force against that, but since turbos can run both methanol and intercoolers... well.
Some could argue maintenance is a worry, but I personally find the turbo is easier to deal with since it uses the engine oil and does not require the same periodic maintenance, given it's treated properly and has ample time to cool bearings before shut down, etc. Both are cool in their own ways, but for my own needs, I prefer the turbo.
After all.... I do enjoy both and they're both great performing forced induction methods. If I had a choice, I'd turbo both trucks just to run higher amounts of boost. If the S/C could pump out more, I'd stick with what I already have, but alas, it is limited.
