The cheapest approach with the most flexibility is a contractors rack. Second best options are the racks made by Thule and Yakima that mount to the side rails of the truck and use the mount holes already provided by the truck manufacturer.
Overall the Thule racks and rack mounts are much better built than the ones from Yakima and there is little or no difference in cost. The Thule version for pickup rail mounting is the Xsporter Pro. A much less expensive version is the Bully rack:
http://www.realtruck.com/bully-truck-rack/
Check with the kayak manufacturer as many are best stored out in the sun upside down and not on the hull (as they will oil can if this is done). If you can go this route then you can take a contractors rack and along the cross braces wrap foam or outdoor carpet and tape it in place and use this to support the kayak. With a cable lock you can secure the kayak to the rack.