Agree with the above. 31x10.5 max. You want 15x8 or 17x8 wheels with no more than 5 inches of backspacing. The less backspacing, the more the tires will stick out.
16x8 can also work, but there are fewer choices of tire size to go with. The largest factory size offered on the TJ was a 245/75R16 on a 16x8 rim with 5 inches of backspacing. This is roughly a 30.5x9.5 tire. The extended Rubicon flares can cover the tread of this and similar tires.
If you put a small spacer lift, say about 1-1.5", it would give you a little extra room to run 31s without costing you much at all. If you keep it low enough, perhaps around 1", you might be able to keep the stock shock absorbers. If you're willing to replace the shocks you could easily add a 2 inch spacer lift.