I have no experience with towing with a T4R. I have a 3/4 ton and a 1 ton truck for towing so I can't answer what is best for the 4runner, but I can attest to the operation and usability of each weight handling system you mentioned.
I've had both types on various trucks. They both worked well when they were in use with a trailer hooked to my bumper. It's the cost factor, the convenience factor and complexity factor that really matter.
Here are my thoughts and experiences on using both types of systems:
Air bag systems: Cost can run the gambit. Base bags with schrader valves at the rear bumper or in the fuel door are pretty inexpensive however, a base air bag setup will mean you have to set and adjust pressures all the time manually. Pressing/venting the bags manually every time you hook/unhook a trailer and having to adjust pressures when out on the road on long trips gets old fast. Getting a more complex system with an onboard air pump makes all of that much easier but costs more. The more elaborate the setup, the higher the cost but the less you have to do to use them. Keep in mind that air bag systems usually specify a minimum pressure required at all times. This is to prevent damage to them from collapsing too much. This can happen because most systems replace the factory bump stops. If you have a manual setup and haven't towed anything for a while, chances are the bags are at 0 PSI and at risk of damage.
Towing specific bump stops: I'll just say Timbren's since they are probably the most popular brand on the market. They cost about as much as a mid-level air bag system for a reason. They work very well under load and have literally no maintenance once they are installed so they are very convenient right out of the box. They are usually very simple to install and only take 30 min, maybe an hour to do. However, the short comings I have found with Timbren's is when the vehicle is unloaded. The increased length of the Timbren means less suspension travel before contact. That's by design so you have less sag but the increased rigidity of the rubber spring makes the ride much more jarring when the stop pad contacts the bumper. On the 3/4 and 1 ton truck versions I have used, the bumper stays in contact with the axle even when unloaded and makes the rearend incredibly stiff to the point it will hop on rough roads. My solution was to remove them when not towing for a while. Looking at the kit for the T4R from Timbren, they specify a 1/2" to 1 1/2" gap between the rubber spring and frame so unloaded shouldn't be a problem on everyday road surfaces.
What it boils down to on a rig like a T4R is usage. How often do you tow with it? How far do you tow with it? How often do you hook/unhook during your trips and for what duration? Etc. Etc. Etc.
If I was in the market for a towing assist setup on my T4R, I would spend more on a mid-high level air bag system with onboard air and wireless controls.
