Went through the same dilemma a few months ago. I've always wanted a Tacoma, but when it came time to pull the trigger, I had to re-evaluate. I would hardly ever use the bed. the first thing I'd probably do is install a cap, just as mentioned. Even then, I usually carry very little. When I do have a large or dirty load, its just as easy for me to hook up my small trailer and use it. I went with the 4runner, below is pretty much the list I made.
Tacoma:
Pros: -Higher towing capacity (even though the 4runner had the same motor/trans, now has a more powerful motor and trans, and the 4runner has bigger brakes).
-Throw the dirtbike in the bed (only if I don't have a cap/toneau cover
- Slightly cheaper (TRD taco vs 4runner trail)
-Manual trans available (big plus)
Cons: -Longer overall, longer rear overhang, more difficult to fit in the garage
-I really have to use for the bed very often
-New motor and trans haven't received the best reviews yet.
-Drum rear brakes? Why?
-No longer a fully boxed frame
4runner:
Pros: -Able to secure items easier, haul people and cargo more easily
-Looks better (IMO)
-Larger brakes stock
-Coil sprung 5 link rear suspension
-t-case lever
Cons: -"only" 5k trailer capacity
-have to use a hitch hauler or trailer for dirt bike
-Hard to find them in the color combo/options I wanted (I got lucky and found one at port exactly how I wanted)
I've been able to work around all of my "cons" with the 4runner, so I am still very happy with my purchase. I was mostly set on the Taco TRD going in because I wanted the off-road goodies (rear diff lock, a-trac, bigger tires). I thought only the 4runner TRD pro had the rear diff lock until I found the Trail. All the goodies, with less of a price demand and a better color (inferno was gone
, Barcelona red is only now being offered in the TRD pro), I have been happy.