I use a Yakima trailer to haul sea kayaks - expensive but works well. For those times when I don't want to pull the trailer I bought a Gumotex Framura inflatable - 14 feet long, 28" beam, performs very well for an inflatable. It is a decked kayak with a cockpit so you can use a spray skirt if you want.
I used to carry kayaks on the roof of a Lance truck camper but that one came with a rack already installed so all I had to do was add a crossbar up forward and it was all set. I'm hesitant to drill holes in my new Itasca so plan to use the trailer or the inflatable for now.
One other possibility is to use a suction cup mounted roof rack - Seasucker has impressive specs, 200 pounds or so of holding force for each suction cup and their surfboard rack uses 6 of them. Maybe I'll try one of those next.
There is also a company whose name I can't recall right now that makes a rack that lets you load your boat at ground level and then puts it (or them) on the roof with electric motors. Costs about the same as the Yakima trailer though.
One other advantage of the trailer is that when we go camping with our usual group of kayakers we can get one of the other guys to pull the trailer to the launch site if we want to launch somewhere other than the campground. Most of them pull camp trailers instead of using motorhomes so they have the tow vehicle available once they get set up at the campground.