OK thanks for all the suggestions. I have a bit more info:
1) There are about 1200 ships in total, spread out over 4 locations, with a total of about 360,000 troops...
2) I've ran some of these ideas by the Archmage of our city, and the Council. It sounds like ships in this world are frequently treated alchemically to resist fire. Acid or other substances might work, though.
3) The Archmage favors hitting all of the ships at once, after they're loaded and at sea, with some kind of devastating and rapid attack. (Nothing specific, just his general idea for how he'd like to conduct the attack).
He's at least capable of casting 9th level spells, and maybe Epic. I doubt he'd personally participate, and if he did it would likely be "off screen" or something... You know how it is... You can't have a guy like that fighting right next to the lowbies, because they'll all die instantly due to collateral damage... He might throw up a Teleportation Circle or something, though.
However, the DM is definitely not shy about throwing shit at us that is much more powerful numerically than the PCs (Not long ago we took out a deepspawn that was casting at least 6th level cleric spells... and yes, it had a bunch of clones defending it, and some of them were even higher level than the PCs...). If we engage this army, I have no doubt that it will be absolute suicide without some really good planning. My character definitely borders on the paranoid, and has backup plans for his backup plans, so I think he'll at least survive... even if he dies.
4) We don't know about their demographics, but we're going on the assumption that they have a similar distribution of casters to our own. Their army outnumbers ours by 10 to 1, and is even greater than our whole population...
5) There is also some kind of very powerful caster/creature that has blocked Scrying (and teleportation?) over the entire inner continent that they are setting sail from (likely an Epic/Deific effect). Luckily this didn't cover the Northernmost tip, which is where my character happened to wind up and witness this massive army and fleet.
My latest suggestion is to attack from beneath the sea, and try and just structurally damage the ships, either mechanically or via Warp Wood or something. The water will provide concealment and cover, and if we're subtle enough we might be able to pull the whole thing off and get the hell out before we're detected. I'm wondering if he'll treat the entire ship as the target for Warp Wood, of if we can go after individual boards... Since Warp Wood has a short range, I'm thinking of using Chain Spell with it... although given how big ships are, and how short 30 feet is, that might not be worth the trouble (I'd have to retrain to learn it, or go on a quest to Rainbow Falls or whatever...)