You did not specify pickup verses 4Runner, nor is it in your profile.... so I'll assume you mean a pickup?
In '89 they had a model change of the pickups (between '88 and 89 model years). 4Runners are a little more ocnfusing because in March of '89, they relased the "new" body style as an early '90 model. So in 4Runners it goes 85-89 and 90-95. This sometimes makes things confusing if you have an '89 4Runner b/c parts stores get it wrong a lot.

In both case, the drivetrain is identical for everything from '85 to '95. The difference is in body stuff, some brakes and electrical things. This means that for the important stuff, it dosn't matter. I think that on this particular sub-forum, people prefer the pre-90s models. That's my own preference too... I don't care how nice and posh the 90s Runnerss are, that will *never* beat out the removable top feature of the earlier generation.