After you sink the boat you can pick the crew up and give them free tickets to Disney Land or throw them in jail it doesn't matter when it comes to dissuading illegal fishing.

The point is to make the expected ROI of trespassing in other nations' territorial waters negative. The crew is cheap and easy to replace relative to the boat. So you have to make the boat go away (sink it or impound it) to make the corporate owner back on land feel the heat.

Imprison them and give them back to their home country ASAP is probably the right way to handle the crew.