Just to give you a response. Yes, the JBL system was an option for both the SR5 and Sport, and i believe standard on the Limited. I have a 04 v8 4x4 Sport with the JBL and love it.
I think part of the problem with opinions is understanding its purpose. If you are the type of person that loves to throw serious woofers in the back in a cage, then probably any stock stereo is going to disappoint. I love the jbl, and with just a little tweaking it gives great sound.
That said. With the cost of aftermarket products being so dang low.. I wouldn't let a stereo be the stopping point. If you find a hella nice 4runner that is missing the jbl, go for it.