I would recommend getting better brakes. I'm new to 4 runners but have had several trucks (dodge) and all of their stock brakes left things to be desired. I've gone to premium brakes from a local auto parts store with decent results in one, Went EBC on another and have a set of power stops yet to install in the third.
If you want to get fancy you can get into drilled/slotted/dimpled rotors to improve cooling, but you could make a great improvement by simply getting better brakes for the same size you have now.
For example my Ram 1500 used to stop OK when unloaded but when towing or needing to stop quickly, it would make you a little nervous stopping. With EBC yellow in the truck now, I'm not worried about quick stops in stop and go traffic.