I am using the Apple cable with my ipod and its works just fine. I read in a pervious thread that your ipod has to be up to date or you could use a flash drive which is a smart way to go.
Check your owners manual. It mentions versions/generations of iPods which are not supported by the 4Runner. I was upset when I found out all iPod Mini's were not supported. So I loaded some of my music onto my daughter's Nano!