If your towing, I would say go for stroker. Gears (IMO) are great for crawling. If your hauling (ha) you need power/speed. Just my $.02.
Why is it then that most factory towing packages come with lower gears and not just a bigger motor?
Think about it this way, for the sake of argument. engine puts out 100 ft/lbs of torque (what gets you moving). in first gear lets say 5:1 ratio, 500ftlbs out of the tranny, 1:1 TC, so 500ftlbs from there. If you have say 3.07 gears, you will have about 1500ftlbs at the axle shafts. If you have 4.10 gears you will have about 2000 ft/lbs. The radius of the tire acts as a lever arm, further changing this number, lowering it the larger the tires is, and raising it as the tire gets smaller.
Essentially if you have 125hp stroker, with 3.07 gears, it will put down 1900ftlbs at the shafts. If you have a 100hp stocker, with 4.10, it will put down about the same amount of tq, the stock motor will just be turning higher rpm because of the lower gears. This is the limiting factor when dealing with improved performance from gears.
In your case, 4:10 and 31" tires with an auto is about perfect if you ask me. going to lower gears would only be marginally beneficial, and you dont want to go that much lower as you will lose some fuel efficiency on the highway, and gear changes will happen sooner.
I think your best bet at this point is the stroker. The cost of setting up new gears will be high, and you wont see as much of a benefit going from 4.10 to 4.56 (11%). THe only problem with the stroker is that it is not as cut and dry as dropping in a new short block. You will need an exhaust and intake to get the most out of it, as well as injectors, and map adjuster to get it to run correctly. some minimal tuning needs to be done.
I currently have stock 3.07's and 31's, with a 4.6, and while I dont regret the stroker, I definitely should have gotten my gearing right first. Even with the added power, towing my boat (2500lbs) isnt that easy on the jeep. It is slow off the line, and I can almost feel the stress in the transmission/ clutch. Ill be going to 4.10's before summer gets here.