There is no one 'best' axleswap for the YJ, especially when you factor in your drivetrain swap, tire size, and the type of wheelin (if any) you plan on doing with the jeep.
The Ford 8.8 rear axle is a good choice for moderate tire sizes, but limits you to the 5x4.5" lug pattern, limiting your choice of front axles.
I went with a front Wagoneer D44 and rear Isuzu Rodeo D44. This gave me 6-lug wheel pattern and disc brakes at each corner. It also allows for 5.38 gears and highsteer up front.
I run 36" TSL's offroad, and they're pushing the limits of the D44's, but it's liveable since I plan on keeping my 2.5L HO. I'd have to look at upgrading if I were to swap in more motor, for the type of wheelin I do in the Midwest.