Corkscrews to drill through hulls or other appendages to affix underwater bombs are some more purely mechanical things to try. Imagine your submarine lurks beneath a treasure ship. By scrying, you can locate a good spot to stick a boarding tube. Pass through the hull via magic, or simply teleport your crew aboard belowdecks. There sits the crew, ever alert for pirates on the horizon, never knowing that the scurvy dogs are already on board!
Be warned, though. Where there are pirates, there are pirate killers. They often are government backed and have far more resources to call upon!
If you can find a book by Richard Zacks called "The Pirate Hunter", it's about Captain Kidd, and Zacks is a very entertaining author. He's got a way of wording things that lands you right smack in the middle of the scene! Great source of inspiration for DMs and Players alike!
You could probably reasonably make torpedoes. Many people think of torpedoes as 20th century inventions, but they made their debut as early as around 1815, when Commodore Stephen Decatur Jr was experimenting with rockets and other propelled explosives.
Actually, the Chinese had something resembling a torpedo much earlier... Um, 15th century, maybe? It was a rocket-powered device with a pointed iron head that skipped along the surface of the water to hit ships right at the waterline.
Depending on how outside-the-box your DM is willing to go, you could theoretically have compressed-air-powered weapons by using either a dedicated air elemental or even several magical air-producing bottles (I forget the exact 3.5 name for those...).
You're right! I had forgotten about those. They made one on some documentary. Here's an illustration:
Oddly, I think they got the idea from an even earlier ancient Greek model that had stability issues. The Greek model, IIRC, wasn't explosive. It's main purpose was as a spiked ramming device. I don't recall how it was propelled, but I recall it wasn't very effective. Like I said, it had stability issues.
Yes I was debating on using a bound elemental to propel torpedoes but the bottle of air is a intresting idea. I was debating on creating grapple arms by using the Craft Construct feat and esseintaly grafting a golem to the outside of the vessel to grab on and attatch bombs or boarding tubes wich would allow my golems to enter the vessel. For some reason I'm starting to invision my ship as a remake of the Outlaw Star for anyone who gets that anime reference. Does anyone know of a way to make a projectile cast a spell on impact? I know that in one book of read of a substitute for scrolls that were called spell tiles or something that cast a spell when you snapped them in half, perhaps I could augment those for use as warheads? My DM rends to let us go rather out of the box provided we can support our idea, that's why I'm here. I need facts to support my ideas.
Contingency, if he'll let you tweak it. Never heard of the tiles, but if he lets you customize a Contingency spell, you can have the spell go off contingent to the tile breaking. Then load the spell you want. (Wooden ships, I'm seeing Meteor Swarm, but that's just me. You may actually want to take the loot before you burn the ship. Always remember, "Pillage before you burn!")
Constructs and undead make good choices.
Also according to page 93 of the Dungeon Master's Guide only fire spells have a problem with water, so wands can make good ammunition. Stormwrack might have more details.