The best Kayak carrier is the thule hullavator. This is the only roof carrier that will save you from scratching the car, especially is you have to load/unload the kayak by your self. Cons, they are expensive and doesn't work neither the OEM bars or the Thule Aeroblade Edge. They require a bar system that extends about 6 inches passing the roof rail.
My second option will be the Thule Slipstream, it has weight and width limitations. but depending on your kayak it may be a good option.
http://www.maloneautoracks.com/ also has some good carriers and loading systems, but they don't seem as strong as the thule systems.
had you consider a trailer instead?