Also use a sword or something. Boats have really good resistance to axes for some reason.

Have four empty slots in your personal inventory. Board the ship, stand next to the mast and facing it, flail away with your axe or a melee weapon.

Destroying the ship in this manner pretty much guarantees that all the material used in the ship's construction will drop directly into your personal inventory.

Try hitting the ship with your weapon. Make sure to do it in shallow waters so you can recover the nails, which will sink.

Originally posted by Science Dog:

Try hitting the ship with your weapon. Make sure to do it in shallow waters so you can recover the nails, which will sink. :cupup:

This is your answer.