After owning a first gen Tacoma and now an FZJ80, this is my .02 on the pros and cons of both. Note that the 3rd gen 4runner has differences like a stronger frame, coil springs all round, and full time 4wd in the later years. Even so, at least some of this still applies.
Tacoma/4runner
Pros: lighter, quicker, more nimble on tight tracks, more practical/economical as a DD, 5 speed manual available, cloth interiors more common, parts/maintenance usually cheaper, usually newer, can usually get into one cheaper
Cons: Weak and rust prone frames (at least on the Tacomas), weak rack and pinion, weak LBJs, sketchier to drive in rain/snow (on part time models), will break more given the same amount of abuse (assuming the same mechanical baseline condition)
FZJ80
Pros: Will take more abuse, much stronger drivetrain, easier to get/fit F/R lockers, easier to lift/fit big tires, more planted on the road, better build quality, can fit more people/stuff, slightly more suspension travel, more stable going over obstacles, comfier ride with coil springs
Cons: Abysmal fuel economy, only auto available, parts and maintenance pricier, faux-luxury interiors that tend to fall apart, older, too big and heavy for a lot of tight tracks, more prone to overheating/brake issues given the same amount of neglect
Tacoma/4runner
Pros: lighter, quicker, more nimble on tight tracks, more practical/economical as a DD, 5 speed manual available, cloth interiors more common, parts/maintenance usually cheaper, usually newer, can usually get into one cheaper
Cons: Weak and rust prone frames (at least on the Tacomas), weak rack and pinion, weak LBJs, sketchier to drive in rain/snow (on part time models), will break more given the same amount of abuse (assuming the same mechanical baseline condition)
FZJ80
Pros: Will take more abuse, much stronger drivetrain, easier to get/fit F/R lockers, easier to lift/fit big tires, more planted on the road, better build quality, can fit more people/stuff, slightly more suspension travel, more stable going over obstacles, comfier ride with coil springs
Cons: Abysmal fuel economy, only auto available, parts and maintenance pricier, faux-luxury interiors that tend to fall apart, older, too big and heavy for a lot of tight tracks, more prone to overheating/brake issues given the same amount of neglect