I ran a bakflip CS-F1 on my old truck and they make it for a raptor. I bought it because I wanted a simultaneous bed cover and ladder rack, and at the time, it looked like the best option. Better than the hitch rack because you can still open your tailgate, making it easy to load the kayaks and gear. Also, I didn't want to put a roof rack on my truck (or on a raptor) because, unlike my euro cars, these don't seem to have dedicated roof rack mounts. However it's ~$1700 for the cover + cross bars, which is IMO kinda pricey for what you get.
IMO, the design leaves a something to be desired, especially because the bars do sway some, but the sway doesn't get crazy even when driving aggressively. I've had no problem carrying as many as 3 kayaks on top (including a 17' rotomolded). I can remove or add the racks in ~10 mins.
For the kayak mount on the cross bars, I use yakima hull hounds. Very happy with their performance.
I'd get something else if I could find another option, but I haven't yet found a better alternative, assuming one wants to keep a bed cover.
I thought a tracrac fits a raptor, but it takes some rigging if you want to use a flip bed cover.