What is the best way to defeat the skeleton armada?

The main thing is supplies. I would say at least 200 cannonballs, 100+ planks, and plenty of fruit and/or meat.

Always try to hit below or on the water line on a galleon if you can. mid deck holes won't come into being useful until they fill up the bottom deck. If you're in a brig or sloop the old trick of scraping alongside them to create holes and prevent them firing cannons is still useful, bailing any water onto the skelly ship. Though keep an eye on your health when doing this, snipers will still be able to shoot you.

If you can gather a lot of cursed cannonballs, they'll come in handy - especially ballastballs for galleons. But really any that immobalise the ship or skellies are useful.

Firebombs are also really useful on galleon mid decks.

If you're feeling brave, one crew member could board, go below and kill skellies that are patching.

Finally, I would say, don't worry too much about the loot from the first few waves. If you can harpoon one or two items before the next wave spawns, fine, but otherwise just mark where they sank on your map and come back later (slim chance it could be still floating if you are quick enough). In the captain wave, identify which ship has the captain on it (the skelly at the helm with the red name) and sink that one last, that will be the one with the best loot.

@mr-creeper-2627

Have supplies I have done it solo with 150 cannonballs and about 80 planks, I suggest at least having near those amounts. You can also use kegs and such to speed it up. The more you have the less risky it becomes.

The main point to the fight is that they do not bail water, meaning anything that adds water to their ship is progress. This includes just ramming them and bailing water into them if needed. In a crew you can also have one killing the repair skeletons by boarding them to prolong the time water flows in.

Positioning is the most important part of the fight. Try to never be between both ships at the same time. Sailing near rocks causes them to crash and focus on your ships survival, in the end they aren't going anywhere if you take a couple of extra mins defeating them it isn't a big deal.

The loot in between the waves might seem important, but they are just trinkets compared to the final captains ships haul. This ship is recognized by a red named skeleton captain. If you want you can have a row boat crewmember to collect the loot, but I suggest you worry about that once you get comfortable with the fight.

If you can park against nearby large rocks do so,as they can only hit you on one side and have to circle the rocks. You can also stack a rowboat full of kegs before the fight,away from your ship and use them to board the skelly ships when they are circling,to do good damage and conserve ammo.

I think kegs, even in the crow's nest, is risky against the ashen fleet. If the mast catches fire, it will go up like a wick and boom!

@mr-creeper-2627
Ram your ship into theirs getting them side by side and then they can't shoot you with cannons. When you do this, you will get a hole or two in your ship. Don't patch them. Keep bailing water from your ship to theirs. Set the sails so you stay next to them grinding your ships together and turn your wheel into them. You will keep your ship afloat by removing water from it while simultaneously adding water to their ship until it sinks. If you want commendation credit for sinking them, make sure to hit them with at least one cannonball.
If it's a skelleon you're grinding against, and you have ballistballs, put a few holes into the second deck since it's all you can hit at point blank range, then hit them with the ballistball. An early firebomb in that mix will help keep repairers off the holes too. You're likely to shoot over the top of them if you use the ballistball first, so make some large holes, ignite them and then ballistball them.

If things get too heated, don't be afraid to sail out of the battle area and recover before going back in. Once a fleet battle is started, it will remain until it's finished.

If you catch a skeletons top deck, cannon area on fire, they won't shoot at you.

As well, everything everyone else said.