I went to lube the brake pedal but once I looked at it wasn't sure where to lube. Cant tell where exactly the noise is coming from, maybe something behind the boot (which I didn't want to start pulling apart)? It does it when I let off the pedal. And is white lithium grease ok to use on it?

I don't think Toyota intended any of these parts to be greased, but an itch has got to be scratched.
There's the hinge, the contact points for the push rod into the master, the spring attachment points, and maybe a few other pivot points. The hinge didn't look very greasable on mine, but it might be oilable. I would try something like Tri-flow that sprays in, (or some molybdenum disulfide grease mixed with oil?) and leaves some dry lube stuff behind if/when it evaporates.
The other points conceivably could be greased; I suggest molybdenum disulfide grease, again because it leaves a dry lube behind if/when the oil evaporates.
I used moly-diS grease(Sta Lube)CV joint grease on the spring attachmant points for my clutch pedal and it has worked very well. Good luck.