I've run 33" tires with 3.07 (5speed) 3.55 (auto) and 4.56 (both). The lower gears helped with either tranny. I'd probably advise going to 4.88 with the automatic or if ya ever thought about going taller than 33".
Don't fall into the trap of going half-way (like to 4.10) and spending bucks on the install, only to be dissapointed later. I plan to do 4.10s, but it'll be with low-cost used gears, my own time/labor, and a tire size cap of 30" on a stock automatic daily-driver XJ.
IIRC in 2000 I paid $129 for the rear (44), and $149 for the front (30RR) - Both Dana Spicer parts. Install kits were $50 ea IIRC, and I did my own labor.. C 8.25 gears are usually higher than Spicer 44, but ya don't need a new carrier to fit the lower gears on that axle.
Shop labor in NC varies from approx $150 to $500 to set them up.