I've been a wheelchair user for 34 years and an avid sailor, so I am well aware of the problems of getting "wheelies" into boats safely. On my yacht I have a boom to swing in off and a 750kg keel to keep the yacht basically stable, but that keel really makes shallow fishing impossible.
Pontoon boats are your best bet and I have a number of friends in the US who own them and love them for lake boats. Even though one is powerful enough for her family to ski behind, she admits it is not a great boat in heavy waves and is best in sheltered waters or lakes.
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I rented a BarBee Boat which was an old Aussie made pontoon boat up in the Gold Coast many years ago (probably 1980s) and that was fine. I could just squeeze on between the railings and rolled around the deck no problems. Had to sit sideways to fit half behind the wheel, but for a standard rental pontoon boat, that's impressive. Was something like these BBQ Boats Perhaps you could contact these hire companies and buy an old one you could then modify to suit, for a reasonable price. After all, rental boats would need to meet 'charter' regs that get stricter all the time.
Another paraplegic I know in Melbourne has another option of a Kiwi designed Sealegs Amphibious boat that he can transfer onto from his chair on land, drive into the water, go fishing, or in his case use a a "tender" for his real boat that has a lift to access the cabins below, engine room, and up to the fly bridge !!! Yes, it is a BIG power cruiser...
Mostly it depends upon mooring/boat ramp/dock facilities and access as well as loading height, but most ramps around Melbourne have been upgraded to have quite reasonable access and floating docks so height is more consistent and would allow roll on/off on a pontoon boat, if the access way of pontton boat is widened and a decent ramp obtained to bridge the gap safely.
You also need to consider the person's weight, mobility, balance and other personal issues. I don't feel very stable in my wheelchair on a small boat as they tend to roll and slide around, even with the brakes on, so you'd need to perhaps consider some sort of tiedown to secure chair or transfer into a seat, which is safer.
I have a number of overseas contacts that may be of interest who have made accessible boats and yachts, so feel free to PM me for further details.
Cheers and safe rolling.