I see you folks are looking at hard tops, but I have seen a soft top on two of my buddies’ trucks that look great and they roll up so you don’t loos any space when you need the bed space. It is called the "Truxedo", I was told about that the dealerships where asking between 550 - 750 for them, but on Ebay.com I see a few for 299 plus shipping. It specifies the 3.0 V6 EcoDiesel for a fit and I think it looks very good on their trucks.
The best way I can explain it is that it has a Velcro system and brace system that is clamped onto the sides of the box, then the cover is attached by the Velcro on those two braces which elevate the cover about 3/4 inch high so water cant flow in (it would have to travel up and in to gain access). The cover also has three braces for rigidity, eliminates flapping. Best of all it locks or latches closed at the very back, so it is locked from inside, so someone can’t just open it unless they want to cut it to gain access.
I am planning to order one in a few days, I can post some picks to give you folks an idea if I can figure out how to post them lol