I've actually given this some thought when I was contemplating of buying a Frontier.
You definitely do not have any space in the cabin for a nice set-up. The only choice is on the bed.
I know you said you do not want it there, but please bear with me. Wiring it onto the bed might not give you as much bass as would in a car. this is because the cabin and the bed are actually seperate. Take a closer look.
My solution is to cut a hole through the cabin and the bed, and then joining them together again. Now depending on how you use your truck, this might or might not be the best solution. Let's say you rarely take it off road(as in really off road, not just visiting building sites), then just patching up the body work would do. Extra measures can be taken in the form support beams across the opening.
If you do take it off road, you can join the cabin and bed together with a rubber wrappng. The kind that you see on modern train ones. Basically the heavy duty/industry/automotive type. this would allow the flexing of the body.
Both of this methods will require that your bed lid to be waterproof, at least the part where you will have the ICE components. And also require a lot of work.
Another way is to extend the space at the back of the rear folding bench. however there aren't that many space you can add hear, and depending on the passenger and music, they might get really sick from all the thumping. You will still have to do some cutting and welding as well, at least it's not as major as the other 2 options above.