A supply boat has white and greenish colors and is the equivalent of a supply truck but does not have to be a replacement for it if the road connection exists. Supply boats have the same capacity as supply trucks which is 8 and require a boat dock as a station they arrive at.
In the Logistics > Transport menu, you can set what kind of supplies they come with and to which docks if more exist. In Logistics > Deliveries, you can also decide where the supplies are unloaded and which are taken away (for example garbage, export materials).
Prisoner Ferry also is known as prisoner transport boat has white and blue colors and it's used for intake to bring in new prisoners if there's no road connection on the map.
On the Connected Island plot where the road exists, it's up to you to decide which mode of transport for intake you want to use. With options available in Logistics > Transport, you can turn on and off intake of prisoners for boat docks, roads, and helipads which will make them arrive only by the mode of transport you want.
The inmate boat has a capacity of 20.
Civilian boats require a boat dock to operate, come and go automatically, and are completely free. They have a capacity of 20.
Transport ferry is a type of boat in Island Bound DLC. Its purpose is to transport prisoners, staff and even visitors between two landmasses such as islands. The ferry operates in a straight line, every 30 in-game minutes, between two ferry docks where only one of them has to be placed by a player. The other one on the other side of the water will be created automatically.
The ferry is able to carry 20 people and can be dismissed earlier if need by clicking on it and selecting Dismiss Vehicle.
To remove ferry, you only need to dismantle/dump one of the docks or the ferry itself.
Note: If the ferry is full of dead bodies, emergency personnel like the firemen will be unable to get onto the ferry. Keep this in mind when making a ferry from the road to your prison and make an emergency way in.