See the Early Ghost Ship Chart page.
The textures and the collision don't line up very well inside this cave. If you have the hookshot and the bombs, you can perform a bomb push clip to access the chest from the starting area. To do so, target the wall on your left when you enter, and line Link's right foot with the black spot on the floor behind him. Then pull out a bomb, wait for it to be fully above Link's head and press b to drop it. This will push Link onto an higher collision. From there, you can simply hookshot the chest containing the Ghost Ship Chart.
If you don't have the hookshot, then you can't perform the bomb push clip above. However, you can still skip entering some warp pots. First climb onto the first warp pot and leaf towards the left side of the railing and jumpslash to get ontop of it. A leaf pump might be necessary. You can then jump onto the next railing and access the warp pot that brings you to the chest.