Just a quick tip.
Do not use the rope directly to the right or left of the helm (steering wheel). Run to the mast of your ship and use the hook to travel up quickly. Now there will be a rope to the right or left of you that Edward will grab as he is jumping off the edge. I prefer using this rope because you are almost guaranteed an assassination because the target will not spot you and evade your attempt which seems to happen frequently when using the one on the ships deck,