Toyota officially states that the FJ water fording depth is 27.5". However, as with some Toyota stats, this is misleading. Yes, you can make a quick run through water at that depth without any issues. However, if you plan on making water fording a sport or sit in the water for a length of time, then this 27.5" is false. As noted above, NONE of the Toyota SUVs/trucks come with a rear differential breather tube. (See:
http://www.toyota-4runner.org/off-roading-home-monst4rs/123-breather-install.html)
Without a breather tube extension, your effective water fording depth is the height from ground to the top of the rear differential. If you do extend the rear diff breather, then your fording depth will be around 27.5". Beyond that depth, you have to deal with water coming into the breather tubes of your front differential, transmission, and transfer case. Also, be careful with your alternator. All of these things need to consider before you even worry about the engine sucking in water.
BTW, the FJ should have the same water fording depth stat as the 5th gen 4runner. The 4th gen may have 0.5" less water fording depth by virtue of it having 0.5" less ground clearance due to smaller stock tires. In general though, i would not make water fording a sport...water is not good for any car for any extended period of time....
