car toppers
It is kind of a pain in the rear to put on an suv. I have a luggage rack that I secured it too with rachet straps, upside down. I used cheap pipe insulation to pad it. I just had this in the garage, I've also used towels, rags, etc. A line to the front bumper keeps the bow from rising while your going down the road and is the only thing you see. It does interfere with opening the rear door all the way, but so will anything else that hangs over the rear. Depending on the type of suv you have and the type of rack, you can buy cross pieces specifically made to hold a john boat or canoe. You can "feel" it up there at highway speeds, but not too badly.
On a pickup with a camper shell, a built in ladder rack would work the same way. I've seen some camper shells with the ladder rack built in and I've seen some where the ladder rack is mounted first on extension brackets and then the camper shell is mounted to the bed with the racks around it. This would be the strongest type and a welder ought to be able to make one up for you cheaply. Look at the way construction guys mount ladders on their trucks, next time you're driving down the highway.
They make pads that go on the gunnels, similar to the pipe insulation I used, so you can mount a canoe or jon boat to your bare roof. Basspro used to have them. The boat is then secured with a couple of rachet straps that clamp to the rain gutter or the window tops.
Here's a link I found on car toppers. It has links to rack makers sites and links to different boat builders sites, including porta-bot and lowe jon boats.
http://www.campinglife.com/output.cfm?id=1049041
Searching on google for car topper will bring up some other links. I had no idea those porta-boats were so expensive, btw. Wow. They been around for 30 years, not 10, like I thought.
Most of the time my jon boat just gets tied in the back of my pickup. I've seen many, many ingenius and not so ingenius car top rigs while sitting in traffic on my way to Nags Head. I've also seen a couple bent up on the side of the road where they blew off. A trip to your local boating store or outdoor emporium should produce everything you need. Just tell them you want a car top rig.
If you know any construction guys with somewhat deeply tanned (red) necks, take a close look at their ladder racks. Lots of these guys have a jon boat they throw up there. They can also put you onto a welder to make you one. We don't all bite, some of us just look mean.
Have Fun