I'm the family cruise editor here. While there aren't any cruise lines which have a separate special needs program, personnel at Disney Cruise Line have said that they do work with special needs children. While they won't be able to devote all their time to your child, it sounds like they'll keep an extra eye out for him/her in the youth program. I have a nephew with Aspergers and I think he'd probably do okay in the youth programs aboard ship. Obviously, you'd be the best judge of your child's needs but we've almost always found the youth counselors on the ships to be caring and personal. My daughter is 9 and has been on 12 cruises and has loved them all!
Good luck and keep me posted on what you decide.
Smooth sailing,
Luisa Frey Gaynor