I have a soft top, so I can,t speak to the roof top mount options. I bought a Thule spare tire mount rack. It works but if you have tele or AT ski bindings your skis might have to be put in the rack side by side, which reduces the number of sets of skis or boards you can get in there. The thing I don't like about the spare tire rack is it leaves my skis exposed to all the muck the tires kick up from the road.
I've come to just flip down one of the rear seats and load the skis in, there's plenty of room with the length of the JKU.
Colorado Jeep Club Member #153