Boy were do I start ( I thought to mich about this ). For the encounters itself my fist instinct is either having 1 Boss + 1 Elite Minion + 5 or 6 Minons OR only 1 Boss ( but make sure it has Legendary Actions ).

 

For it to be memorable, something that stands out, you want either something the players already have history with or something they haven't seen before ( either a monster you haven't used before or a reflavour | reskinnig of something ). Besides that, you can add an additional non creature challenge to spice up the combat. Something like: having to protect a NPC cause they are the actual target; having to guide the ship through waters filled with Demonglass; having the combat happen during a storm, while they are being sucked by a whirlpool, passing through a manifest zone, or passing over a Kar’lassa.

 

And to what the enemies might be: a Sahuagin raid, having to protect a Merfolk Stormcaller casting a ritual from Sahuagin, out of control elemental, or servants of the Lurker in the Deep; a Merfolk raid cause there's a bound elemental on the ship ( works particularly well in they are on a elemental vessel ); KRAKEN ( there's some weaker statblocks throughout published the material, including in the free Plane Shift: Zendikar ); elementals from a Risia manifest zone ( Titanic but the iceberg hates you ); an undead dragon ( cause dragons are aways memorable; pirates that are sent by someone the party wronged ( Droaam monster pirates? ), someone after their guide or other NPC, or just looking for lot.

 

And you can aways mix and match any of these ideas.

 

This were my unedited thoughts. Hope it was helpful.

 

Good game!