Boats are a good idea. They are mobile and silent when the engine is off.
The problem is they have to float and stay more or less dry on the inside. A canoe is light weight, quiet, can carry a bit of cargo and travel in shallow water but it can be sunk easily. Boats that are built to be hard to sink require power to move, require deeper water and just don't go very fast. That means you have to stay out of range or you are a big, slow moving target. An engine requires fuel, and a lot of it and you need to be able to get more fuel and a lot of it. Steering mechanisms and props are easily damaged so they need to be protected from sunken logs, cables, nets and other debris.
I think a "survival" boat that could carry a number of people, food and water to keep them alive and enough fuel to keep them mobile could be built but it would have to be engineered to be low in the water, wide beamed, and low angle structures above the water line to make it more bullet resistant. It would need long range fire power and a way to desalinate water and perhaps use brown gas or hydrogen for fuel. A set of retractable hydrofoils for those times that you need speed more than stealth might be worth the trouble. You have salt for trade and fish could be a good barter item when you have to go into port.