I would lean more towards the 4.56 if you have a Overdrive transmission. If it is an automatic the 4.10's is the lowest option you have unless you never plan to get over roughly 55 mph. The pinion gear on a 4.10 will generally be stronger than that of a 4.56 of the same brand. I would look for original 4.10's out of 4 cyl that are as close to new as possible. You just can;t beat the Dana/Spicer gears for reliability and fit perfection.
94 YJ 4.0/3spd dana 60/44 w/35's 9" of suspension lift
Sold-06 TJ X 4spd auto 3.73