What size tires did your Tacoma come with stock? and what R&P gears did it come with stock? If you want that power I would match that combo to the size tire you have and get the gears that match.
Differential Gear Ratio Chart - Tire Size to Gear Ratio
I don't know the Tacomas as well, someday I would like one. I am running a 92 with a 22re and know those well, so sort of similar. With the 22re 4.88=33's and 5.29=36's is pretty much right on the money back to stock power band as if you were running 28" tires and 4.10 gears.
22re hp = 112, torque = 142 #
2.7L hp = 150, torque = 177 #
3.4L hp = 190, torque = 220 #
Looks like you are right in the middle of your old set up and mine as far as power goes. I know the little 22re needs all the gearing it can get. I envy the engines in the Tacoma trucks.
In your old truck you had a auto which east some power. Also it does take some power to get those big tires moving. From what I have been told the 3.4L engine does not require as deep of gears as the 22re because of the increased horsepower.
If you like the power of 31's with your 4.10 gears then 4.88 is probably the way to go. You are really only talking about 300 rpm between the two setups you mentioned. If you go w/4.88 you will run 100rmp less than stock, or w/5.29 200rpm more than stock. That is based on a 28" tire and 4.10 gears so if your stock tire size or gears are different then adjust.
Also think on the plans of how you plan on using the truck in the future. Towing, winch, bumpers, campers, toppers, roof racks, etc. Do you potentially see yourself going to a bigger tire down the road. Do you put on smaller tires on for winter? Is this a DD, commuter, or trail truck.
Drive around on with the truck at the rpm's it would be at highway speeds with the different gears and see what you like best. I don't think you will notice too much power loss in town, I think the larger difference will be at the highway speeds.
Try to drive others trucks if you can, or see if someone has a used or extra third member already set up so you can just put it in the rear and go for a 2wd test drive for a while. You can also set up just the rear end with 4.88 gears and drive in 2wd for a while. If you decide you like it you can then gear the front. If you don't then you can gear the rear deeper and try it out. Then you are out less money if you do not like your first choice. You can also re-sell the barley used gears to recoup $ if needed.
Good luck on your choice and let us know what you go with and how it works out for you.