I've had 2 4Runners (98 Limited & 02 Sport) and now a Tacoma DC, so I'll throw in my 2 cents.
99-00 4Runners had the manual option. 01-02's did not. Also, 01-02 4Runners did not have the rear locker option, but came with an AWD system and a CDL (center diff lock). But the 01-02's did come with VSC and TRAC, which proved to be really useful, especially in snow. If your wife or children are going to be driving this, VSC/TRAC would be a good option to have.
The only reason why I sold my 4Runner for a Tacoma is because I needed (READ: wanted) a bed. I hated cleaning off skis, boots, dirty clothes, etc. when putting it into the 4Runner, then having to smell the muddy clothes or whatever on the way home. Also, I wanted more room to carry mtn. bikes and cargo. The 4Runner COULD have done this, but I knew I was going to destroy the interior, and if I were to go with 1-2 people, cargo area would be a problem. (I did not want to get a trailer or some sort of a hitch rack to carry my stuff.)
That is the sole reason for my switch.
I will add that the rear room in the Tacoma DC seems to be a tad bit smaller than the 4Runner, so your rear passenger occupants might be a bit tight for space. Also, not having the open rear cargo area like the 4Runner gives it more of an enclosed feeling.
If you do not NEED a truck bed, the 4Runner is awesome. If you have lots of cargo to carry for trips and whatnot, it's hard to beat a Tacoma. Plus, Tacoma's seem to hold their value a bit better than the 4Runners. But I will say that the Japanese made 4Runners seem to have a better build quality than the Tacoma's. The Tacoma seems to have a tiny bit more creaks and rattles, but nothing I can't handle.
Last note: If you're looking at a 4Runner, you might also want to check out the 4th Gen's (03+). For on-road travels, they are WAY more comfortable than 3rd Gen's (96-02). The prices are coming down rapidly on those, where you could probably pick one up for just a little more than the 3rd Gen.