If you want to off road ditch the running boards, your going to have to do something crazy to hit the rocker panels on a 4 runner. The running boards easily get damaged and do not provide much protection , I've herd of people damaging the rocker panels from the running boards buckling into them, where as they could have done the same obstacle without them and cleared it.
Stay on the road, keep boards. Go off, ditch them quick. Since your asking this question read up on a lot of basics about off road driving before you venture out, tire pressure, gear selection, entry and departure angles, walking terrain, ect.