Pirate ship? That changes everything!
So is this a "defend the beachhead/port from undead pirate zombies" scenario a la Pirates of the Carribbean?
I've used waves every other round and that seemed to work well, typically between 2-4 waves of monsters, each wave worth about an encounter level equal to the PCs. I like to include a trick which stops the waves of minions, sort of like your burn the boat idea. For example, the zombie pirates are coming ashore in canoes from the main ship (which is somehow life-linked to the leader?), so the PCs can take actions which stop the zombies from ever reaching the shore... firing a cannon/balista, raising an anchor chain/defensive net, grease spells over the surface of the water + fire, etc.
Another possibility is to signal waves with some effect, like a war horn, a pulse of necromantic magic from the masthead, magic mists which whisper and glow for a moment, that sort of thing. You can provide cues to the players this way about when to expect the next wave. And the effec can include a progressively more challenging environmental effect which favors the minions.
Oh, the spectral tendrils from the DMG seems like a good addition, especially if the PCs need to move between different areas between waves (eg. the zombies assault different areas of the port).
Lastly, if you're using a bunch of minions either mix in a couple goons/super-minion, add an extra minion or two for every 5 you include, or give the minions a trait which imposes a cumulative effect regardless of attack rolls. A good example would be the Hanged Ones which immobilize when 3 or more are adjacent to the same creature.
Good luck.