I realize that your post is from February, but I just read it. Having traveled to Guana on my way to Scotland Cay AND being a resource teacher, I felt I had to respond.
It is easy enough to get from Florida to Marsh Harbour, but you will probably be on a small prop plane, not a jet. This may cause some level of discomfort for your son, depending upon where he is on the Autism spectrum. If you think your son can handle the noise, pressure, and turbulence, then absolutely go for it.
The taxis at the airport are helpful in knowing the departure locations and times for the ferries. They will also wait for you while you shop in the grocery and/or liquor store. The ferry will be about $15 per person one way. Again the stimulation is something to consider. It is a 20-30 minute ride from MH to Guana with wind noise and some bumps from the waves.
This is an extremely friendly and tight knit community. If you want to or need to make it known that your son has Autism. I have absolutely no doubt that everyone will do what they can to look out for your son and keep him safe.
In terms of where to stay, most homeowners will certainly take a few minutes to answer any questions you have. Another good source of information are the caretakers for each rental home. They can provide up to date information on details of the house. I'd encourage you to double check anything that the house offers, like AC or satelite TV, is currently operational. I've only heard of one house being less than desired. However if you are depending on a certain feature for your son's comfort, you need to make sure it is in working order.
Consider staying with a property that is somewhat away from Nippers, which is on the ocean side but directly East of the settlement. I understand that it can be a bit on the loud side.
One last point of advice, be sure to hold on to enough cash to get you off the island. (Although it would be a perfect island to be stranded on.) It will take another $15 or so per person for the ferry, cash for the taxi to get to the airport, and there is a $15 or $20 per person departure tax from the airport. There are NO ATMs on Guana.
Good luck and have a wonderful time! My family and I are planning to go in June!