Friendly with Pirates for "Up to Snuff," Can't Complete Quest

If you are on the quest Up to Snuff but still friendly with the pirates who have the snuff, you must complete the quest Attracting Attention which is from Captain Keelhaul on The Riptide. If you don't see the quest on your map, go to the ship and you should be able to accept the quest once you're aboard. Completing the quest should allow you to kill the pirates and obtain the snuff from them.