This seems to be a fairly common peril in movies, but the only ones I can think of are...

20,000 Leagues Under the Sea - squid attacks sub
Voyage to the Bottom of the Sea - squid attacks sub's divers
Octopus - octopus attacks sub and cruise ship
Peter Benchley's Beast - squid attacks sub and boat

Are there any others?

Deep Rising

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It Came from Beneath the Sea.

I know there was a giant octopus on land in one or more of the Toho Godzilla movies, can't quite remember if one attacked a ship at sea.

Tentacles (1977)

I immediately thought of the Octupus in Popeye, but I haven't watched that in a long time. Did it attack a boat?

Isn't the Kraken from Pirates of the Caribbean: At World's End, sorta like an octopus?

I don't know, I think it's some kind of fictional derivation of an octopus.

I had also found Kraken: Tentacles of the Deep when I was looking for these movies but I don't know exactly what that kraken was. It was described as "octopus-like".

Maybe, but if you're looking for a scene with a giant aquatic beastie with tentacles causing destructive havoc on a ship, that's a good one.

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Sharktopus

Not a sub or boat, but Sphere.

War of the Gargantuas.

Warlords of Atlantis

Doesn't an episode of Wild Wild West have a giant octopus? Or mechanical one?

Steel Magnolias

Atragon

Thanks for the titles. I sure thought there were more than that but I guess most are just fictional derivations of the actual animals so there's not too much to worry about.

The Beast

Reap The Wild Wind

Endless Descent has a giant octopus and also a giant amoeba lifeform trying to eat a submarine.

WAKE OF THE RED WITCH (1949), another John Wayne sea adventure, also has an undersea battle with an octopus. (Well, IIRC, it was a squid in REAP THE WILD WIND.) That's the film whose octopus was in storage and it was stolen by crew members for Ed Wood's BRIDE OF THE MONSTER (1954) for the scene where Bela Lugosi struggles with it. But they forgot to take the mechanism that MOVED the octopus, so poor Bela had to move the tentacles around himself in that memorable "action" scene. Didn't they recreate that bit in ED WOOD?

Yes and did with boat that with Swee' Pea and then Popeye attack octopus.

The Atomic Submarine(1959)