I agree with FJeddah and most of my stuff has come from vendors here, but keep your eyes on the buy/sell part of the forum here as well. A lot of the forum members put up great deals on used parts. Finally your local Craigslist is useful too. I've gotten stuff from of the above.
ive personally ordered from toytec, springtailsoultions, tirerack, 1sttoyotaparts, trdparts4u, trailgear, ellis precision... all with great service. if you stick to the supporting vendors you cant go wrong.
make sure to factor shipping costs in before you buy.
There isn't really a "one stop shopping" point for the FJ like you have for Jeep with Quadratec.
It really depends on what exactly your looking for as to where is the best place to shop for it. Most of the aftermarket parts for the FJ are best bought directly from who manufactures themselves. We currently have the vast majority of them as supporting vendors here.