It tracks better because of longer wheelbase (at least 18 inches of difference), which has its own drawback, such as worse break-over angle. Your 4runner is 17 years old, lots of stuff can affect highway stability: lower control arm bushings, tie rods, steering rack play, steering wheel intermediate shaft play, alignment.
If any of the above is badly worn, a brand new Tacoma will track better on highway. A brand new 4runner will also track better. Even a 2006 4runner with brand new steering parts and proper alignment, will track better.