Scion radios (made by pioneer) are plug and play in the 4runner (no extra wiring harnesses or adapter kits needed) and allow you to maintain steering wheel controls. They also sound better than stock and have an attachment cable that lets you plug in an ipod. There's usually a few floating around the classifieds here or on some of the scion forums. It's a nice, cheap, effective route to get better sound and ipod functionality.
I love my USA-Spec ipod connector that integrates with the factory system. I have full functionality of the steering wheel controls. I can buy an adaptor from apple to update the connector as well
My 04' :driving:Runner had the JBL and it was great until the CD player stopped working. I replaced it with a Kenwood unit that streams music and has the hands free calling. Love it and it was pretty cheap.
:driving:
Not all 4th gens have a 3.5mm jacket stock in the center console I take it? Few bucks for a cord at Radio Shack and iPod is hooked up. I'm not a crazy sound hound though, so I'm sure there are better hookups.
I put the same USA Spec iPod adapter in my 4Runner and love it! Also used the AUX input on the adapter and added a 3.5 jack in one of the knock-out blanks on the center console.