I would suggest getting a taxi ride. DO NOT do the water ferries! They are Titanics waiting to happen and are tourist traps (one cost for the ride, then a hidden fee for the unannounced tour guide). Taxi's are around $4.00 a person each way.
Just an FYI, Nassua and Freeport are not ADA compliant. You won't find many curb cuts and the taxi's are vans that they cram as many people into as possible. A wheelchair that folds up might be able to get into the taxi. There is no way that a
ECV could go in one. I think there is one wheelchair accessible van on the island that runs for around $40 each way. I am not trying to dissuade you. Just trying to warn you as to what you might run into.
You might try calling the cruise line and see if there is anything that they can do to help.
Once you are at Atlantis, it is mostly handicapped accessible. There might be a few places that will be difficult for you.