You're comparing a modified 22RE to a stock 3.0 and that is not a straight up comparison. For every dollar you put into a 22RE, the same amount put into a 3.0 will still give it more power and torque and be a more drivable engine day to day. Ivan Stewart raced the 3.0 for years and made tones of power.
Not quite. For one thing, you can't touch Ivan's motor for what we all have in our bank accounts put together I should think. I do NOT know, but would be willing to wager, that Ivan's heads are not very much like any of our 3.0s are/were, thereby fixing the major 3.0 problem. $$$$$! Also, for every dollar put into modifying a 22RE, it takes two dollars into a 3.0 to produce half the result on a percentage basis. Those who have mildly modified 3.0s on this board have been disappointed, while the similar level of modification on a 22RE satisfies - and is cheaper to boot.
If money is no object, then drop an LT1 Corvette motor in your 4Runner and never look back.
Out of the scope of the question though.
There's a rational limit to how far you can go with either a 22RE or 3.0 and still be emissions legal for daily driving. So asking which engine is better is a moot point. What do you plan to do with your next vehicle? Rock crawling, towing a 1000 lb boat, 50 mile commute each way? Personally, a supercharged 3.4 Toyota swap would be the best solution to keep it all Toyota.
Agreed, the use is the determiner. And also agreed, the 3.4 (even normally aspirated) fixes all the 3.0's problems, every one. But its out of the scope of the question.