Yes, it will fit. Is it better? Probably. The FJammer is a very good stereo. The stock stereo in the FJ (non-upgraded to the FJammer) is the same stereo they put in the mid-level 4Runners.
In case anyone wondered, the JBL unit in the later model FJ Cruisers will also fit. I swapped my JBL CD/Cassette head unit for this FJ Cruiser JBL 6CD/BT/USB unit. I actually really liked it, but it was damaged in shipping so after putting it in, I pulled it back out and got my money back