They are both good engines, both have their advantages and disadvantages. I'll try to cover them both...

4cy, 22re....

Pros:

Easy and cheap to work on
Good power, for a 4cy
Decent mileage if properly maintained, 18-22
Bulletproof if properly maintained
Parts are plentiful, and decent aftermarket support


Cons...

Poor mileage is improperly maintained, 12-18
If timing chain fails, more than likely it will cause major engine damage
If overheated too many times, head will warp/crack
Underpowered in a 2nd gen heavy 4Runner



6cy, 3vze

Pros....

Good low end power, good improvement over 4cy
Bulletproof if properly maintained


Cons...

Difficult to work on. Definetly not designed with the the mechanic in mind.
Poor fuel mileage most of the time, 12-18
Problematic head gaskets. Usually hit or miss, some have problems, some do not
No aftermarket support



If you have any more questions, ask away



The price of 3rd gen 4Runners, 96-02 have come down drastically in the past few years. You can get a decent 96/97 3rd gen for $4500-$6500. 4x4, 6v, auto. I bought my Limited 97 for 6600. In VERY good shape. Leather interior, power everything. Real nice. The newer 5vzfe V6 (and the 4cy) is leaps and bounds better than the previous v6. So smooth, good power, and much easier to work on. Rides like a caddy compared to earlier models.