You going to run it on there 24/7 or just for trail rides? If just for trails I would go taller... but if you keep in on all the time the shorter one may be better.
I run a 3 foot on a spare tire mount bracket and it goes about 6" past the top of my jeep. I still have to take it off for my garage or parking structures. My opinion is get the 4 foot and put it on a quick disconnect and run it when you need it.