Stock for stock and the same driver, your base model Wrangler isn't any more capable than a 4Runner. It'll get up some stuff the 4Runner can't climb, and vice versa, depending on whether the specific obstacle favors a shorter or longer wheelbase. An elocked 4Runner will probably make it through more stuff than a base Wrangler. On the other hand, a Rubicon is super-capable with front and rear lockers and a low range tcase and will mop the floor with any stock 4Runner, elocker or not.
Start adding mods and it all becomes meaningless though. Lift, tires, lockers, etc, all game changers. It might be a little cheaper to mod the Jeep than a 3rd gen 4Runner? Dunno. I guarantee it's cheaper to mod my 1st gen than to mod a Jeep, that's all I care about (because #brokeassrustyYotaguy).
This does not factor in reliability. Jeeps break more parts and have more engine trouble, in my experience.