Up until recently (like the last two month or so) there was really nothing for power or tuning for the 1grFE dual VVTI. The only option for more get up and go was gears. And boy do these things need that when you pile on the weight and tires...
Anyway, things have changed recently... but its sort of go big or go home...
Two supercharger kits have hit the market. Magnuson and URD. URD is claiming something like 130RWHP gains at 5.5 PSI and magnuson is more like 80-100 RWHP. To put that in perspective, the URD claim would mean well over 400hp as a factory HP rating. The Magnuson one does include a powertrain warranty (I think) if you have a new vehicle. I have the Magnuson on mine, but I have 80k on the truck and no warranty.
For tuning... There are a few things. Magnuson has the keys and they tune the ECU (they were basically the TRD kits before anyway) , there are also a few tuners (two that I know of) that supposedly have a way as well. Although, I have not heard of them actually tuning a 5th gen. They tune lots of Tundras.. and claim they can also tune the 1grFE... However, non of them have canned tunes available yet that I know of.
URD uses the piggyback approach where they have an ECU that sits in the middle and does the fueling and timing for the supercharged setup. Think it is called the UCON-EMS.. For more minor stuff they have a MAF calibrator (but that is just going to be small tweaks).
Bottom line, the air intakes and what not will make no real difference, but things are changing now (finally, after many years of waiting)
The reliability of these kits is still obviously in question. At only 5-6 psi it should not be a problem with the right tuning. The motors seem to be pretty strong, but they do have high static compression and pretty lightweight pistons. Plus you are talking about 5-6k at least for a supercharger.