both are capable vehicles. i think the fj sits slightly lower but very insignificant.
some differences though:
1. front diff is 8" vs the 7.5". this means stronger front end (including the axles) and the associated parts.
2. atrac system is much more improved (I'd say in the magnitude of like double digits) and even more fine tuned compared to the 4th gen 4runner.
the fj may lack the initial vertical height but does gain a more powerful atrac that helps. w/ both vehicles lifted, I'd go with the FJ if both were free