The best method to grind ships is to take your most powerful ship (the Abyss) to the first region and fight all of the battles with multiple enemy ships. Fully upgrade your ship and choose perks that will help you most, similar to as follows:

Sail: There is not many perks in this category that are useful, so it is suggested you choose those that will increase your speed to increase the rate at which you move across the map. Options include High Spirit (increase speed 10% during daytime) and Full Speed (increase speed by 10%).Figurehead: Again, not much here is at all useful. The Eagle Eye perk is suggested (reveals a weak point on enemy ship for criticals).Hull: This is the most important set of perks. You should tune the perks to match the opponents you will be facing most frequently in the first region, basically small sailboats. The most effective attack against them will be the canister rounds. Recommended perks include Brute Force (15% overall damage boost), Canister Pro (increase canister rounds by 60%), and Critical Shot (increase crit change by 10%).Cannons: Not a terribly useful category, but Critical Strike is recommended (next attack will be a critical one).

From the region-selection screen, choose the first region, Scorpion Reef. Move around according to the image below, starting from the Spawn Point. Fast travel when specified, and manually move your ship by drawing paths for it on the map when noted. Once in battle, be sure to skip all cut scenes. As the battle begins, use your Spider Shot immediately to break the enemy attack. When it is your turn, fire away. Use the canister rounds first to take out one ship. Then hit the next ship with the gun, followed by the cannonballs. This may destroy two ships, but if not, you will get another chance with your canisters before the enemies next turn. The only battle that may proceed into a second round is the one battle you fight three boats. To prevent this, save your ability (next shot guarenteed critical) for the second battle (i.e. don't use it in the first battle from the picture below).

Following this route will destroy 15 ships in 4.5 to 5 minutes, including all loading screens. At this pace, you will net around 180 to 200 ships per hour of playtime. After completing all other achievements, you are looking at a solid 3 to 6 hour grind.