Here you see the Tellerium Shipwright and Yard.  Notice the absence of magically aided construction.  This does not hamper their shipbuilding, they are quite used to building sturdy vessels due to the maelstrom's proximity...

Other Docks

Locales that offer berths, without Shipwrights.
The below dock locations do not offer the perks that shipyards at the major townes offer. Your crew's morale is not restored and you can't repair or refuel here.

Pirate Hideouts
  Pirate hideouts are spread throughout the world, each pirate faction has its own hideout in either Alyria or in the Underground.  You can contract crew from these berths, currently all hideouts contract sailors at 1,460 gp.

Pelican's Demise
Three Bearded Jake's
Daggerwind Reef
The Angry Whale
Smuggler's Cave
Frigate's End

Villages
 Here are the known lesser dwellings of Alyria that have water access.

Jalur Lumber Camp - A lumber jacking village on the far northeastern portion of Avros
Mulakanathos - A village on the northern coast of the southernmost river on the eastern side of Beltane.
Palamire - A Village on an island southeast of Auryn.
Gilvery - A Village southwest of Desert Thorne.
Unknown village - A village on the large island between Auryn and Beltane.
Unknown village - A village on the peninsula between the 2 eastern rivers of Beltane.

Secondary Docks

Irda Isle - Offers berths for ships inside of the Irda Reef.
Seahag Isle - Underground Location.
Hotel Hello - Underground Location.

Clan Halls with Docks
Clan 37 - on the western coast of the island northeast of Arcane.
Clan 81 - on a small island south from the Southern Sigil Docks.