Good for you!
I took an ACA adaptive paddling workshop a couple of years ago. They have information at:
http://www.americancanoe.org/getgo/adaptivepaddling.lasso
The big issue for folks with lower-body disabilities is keeping them stable in the boat. The simplest adaptations are to add foam to the sides of the seat for lateral support, and to build up the front edge of the seat to make it more of a "bucket". Build up a bulkhead footrest because he won't be able to feel pegs. Building up a higher seatback often helps -- it depends on the level of the injury. You might also want to pad the seat bottom and anywhere his legs might hit the interior because when there's no sensation it's easy to get cold and bruised or develop pressure sores. It doesn't have to be pretty at first -- you can duct-tape foam in place while you're figuring out what works. Just make sure that he can easily wet exit when you're done.
Sometimes it's easier to get rid of the stock seat and build a new custom seat. It's not hard to glue up and carve one out of minicel. Some folks have tried using self-expanding foam in a bag to mold a seat to the body. Be careful with that approach -- some of the foams give off a lot of heat when they kick, and someone with no sensation in their lower body won't know they're being burned.
As for boat selection: Almost anything will work to get him on the water, but for a boat of his own a 60-lb 6-year-old is going to have a hard time with an adult-sized rec boat -- it's too wide and too deep. I'd think the Perception Acadia Scout would be ideal to get him going. The Ocean Kayak Kea, Perception Carolina 12XS(the old 12.0), or Jackson Rec Mini Tripper might also work well. The WS Tsunami SP is nice but more expensive. He'll probably have a slightly higher center of gravity than most kids his size because of the decreased muscle mass in his legs, but a bag of water ballast would be an easy fix if it's a problem. He's probably got better upper-body strength and coordination than most kids his age and will pick up paddling skills fast. If he's comfortable swimming he'll be a lot less worried about tipping over than the adults.
A proportional small-shaft paddle will be much more comfortable than an adult paddle for any six-year-old. There's the Bending Branches Minnow, Werner Sprite, and others.
Don't be nervous. And don't be afraid to ask the boy what works -- he's the expert on his injury. Just get a heap of assorted foam, some duct tape, and have at it.
Good for you!
http://www.kayaker.com/new/products/boat.asp?type=recreational&ID=124
http://www.oceankayak.com/kayaks/single_kayaks/kea.html
http://www.jacksonrec.com/news/article.cfm?article=200706151
http://www.bendingbranches.com/woodkayak/wk_minnow.html
http://www.wernerpaddles.com/paddles/sprite.html