I currently have a 2017 TRD Off Road, and my brother has had three JKU Wranglers of varying trim levels, including the Rubicon.

Yes, the Jeep, both stock and modded, will be more capable off road. It's just a better platform for that kind of driving, there's no getting around it. However, it's a dog on road, my brother used to say it was "like throwing a brick into a hurricane headwind." They're just not that comfortable to drive because of the sacrifices they make to be capable off roaders. This includes everything from driving characteristics, to seating and interior space availability.

The 4Runner on the other had, is much more comfortable on road, as you know owning one yourself. Still a very capable off roader, and can get you there and home with ease, but the Jeep will always be better off road.

It really just comes down to how you use your vehicle most often. Once you've answered that question, the choice becomes pretty apparent as to which you should go with.