The majority of owners here will suggest the OEM tonneau cover. It's functionality, durability, and versatility seemingly cannot be matched. However, one downside is price. Your best bet would to try to get the dealer you're buying from to include it, if they have one in stock. Otherwise, you're looking at over $800 for a new one or around $400 for a used one of this site. Variations such as Advance, Versacover, or Pace Edwards may suit your needs for a much smaller price. A snapping tonneau cover from Ford is only $300 I believe. Rusty at Spartan Ford can answer all your questions if you decide to go that or the OEM route. Also, if you do a search for "tonneau" you'll get tons of info on each brand available.
Personally, I would look into a fiberglass cover (ARE, Leer, Snugtop, Gaylords, etc.) They may not be as functional as the multi-fold OEM, but I think they look better. Again, price is a concern, with a new one going for about $1000 painted to match the exterior.
