Starting in 2001 for the third gen, it was auto only. The 4th gen was never offered with a manual.
Tacomas have 6-speed manuals as well. Rear locker is available with the Off-Road package. But the FJ Cruiser with the manual transmission are full time 4WD rather than part time as with the Tacoma and FJ Cruiser with an auto.
In 2000 when I was looking for a 4Runner, I didn't see any manual transmissions, not a one and I looked at a lot of 4Runners. Customers just didn't want them. Then in 2001 they dropped the manual transmission. Some people thought it might of been because they offed VSC and a manual wouldn't work with that. Well, Toyota does offer VSC with manual transmissions in other vehicles, I think it is that it wasn't a big seller and they dropped it.
I didn't realize they stopped making them in 2002. Thats interesting. And as for the fj, I'll probably head in that direction. Right now I have a 1990 and love it, but I'm nearing the land of buying my first new car and not having a manual is enough to get the 4runners little brother..