As many have said before, a lot of the decision between a stick and an automatic is personal preference. That said, for me, the automatic is very nice for off road use. If you're planning on doing tough trails, particularly rocky trails, I think the automatic is much easier to drive. If you have to stop the vehicle while you're perched up on some rocks trying to figure out your line, it's a lot easier with an automatic. With a stick, you might have to kill the engine. With the low gears we run, you can always restart it in gear and continue on, but I still think it's a lot easier with an automatic. Of course, others have the opposite opinion.
I think automatics are also a little easier on the drivetrain than a stick. Regardless of your choice, you will probably want to change your gear ratios if you run tires that are somewhat larger than stock. Low gears will make a huge difference in your 4 wheeling experience.
If you aren't planning on heavy duty off roading, probably either transmission will work fine for you.