Originally posted by Lucidess:

Store boats in a Chest, and label the chest "Boat Chest".
Your welcome.

However you still have to be careful. Mobs will attack the chest and break it. Then the items on the ground are subject to despawn if there is no nearby workbench.

My advice is to bury a workbench near the chest. That way you will not lose the workbench or the items if mobs break the chest.