After Indiana Jones? Golden Retrievers tend to be adventurous, and I'm pretty sure Indiana Jones went out in the ocean at one point...

Otherwise, how about Nino? You know, after 'El Nino', the underwater current?

It'd be cute...but then we wouldn't get to suggest names.
Pirate was good. Maybe Skipper? Tsunami? Cyclone? Bosun?

I like "Pilot" for non-nautical reasons all my own, but then there's the Japanese "Anjin." That's what they call John Blackthorne in "Shogun," because they can't pronounce his name. {= )

If you want to name him after an awesome character from a relatively obscure fantasy epic, you could call him Saltheart Foamfollower or Pitchwife. Of course, you might then want to read "The [First, Second, and Third] Chronicles of Thomas Covenant the Unbeliever," if you haven't. It's worth the author's redundant and sometimes condescending prose, and the main character[s]'s unrelenting angst, to get to know some of the other people in the world.

Um... there's Nautilus or Urchin or Limpet or something like that... Oh, I know! Pagoo, after Pagoo the Hermit-Crab. ^_^ Or maybe Sebastian, which I think is actually a cool name.

Someone said Kraken... following the train of thought, there's Leviathan, Selkie, Narwhal, Triton, Neptune, Odysseus, Ulysses, Argo[naut]...

That's all I've got right now.

~Neshomeh

...or I would have said go with "Davy," since it's a good alternative to "Squid." ^^ And some people might not figure out who you named him after unless you told them...

Besides that, I'm rather blank on nautical things- well, barring "Cthulhu," but I doubt your dad would like that one too much either.

(I personally think "Squid" is good. Hmph.)

Or Ahab?

Shame because it's also the title shared by some awesome otters. Maybe it'd be better suited for a labrador ...

"Sharky"? "Silver", as in Long John? Bonney or Read (surnames of famous female pirates who I think were cool)? No, maybe not the last two - Bonney sounds girly and nobody would get Read. Edward? That was Blackbeard's real first name.

Submarines are nice.

Flipper
Navy
Swimmer
Siren (because they lived in the sea...)
Triton (as in the merking)
Neptune

Oo! "KRAKEN"! That's not a MAIN PotC character...

Or, owing to my current Narnia indulgence:
Caspian (the Seafarer)?

I'll keep it in mind, and maybe add more later.

Huan!

Or, how about "fluffy"?

Ooh, this should be fun.

While we're going along with the sea-themed names, you could always call him "Skipper". Or "Osprey", which is a fish eagle. Or "Bosun" or "Buccaneer" or "Doubloon" or "Freebooter" or...yeah..."Dolphin"...even though that would be weird...um..."Oakum"..."Pilot"...

Yeah, that's all I got. *shrug*

Here's some others:
Pirate
Marine
Galleon
Parrot
Commodore
Admiral


Though if you used those last to then there's a possibility that Sailor might feel inferior to the new puppy, but since I doubt he actually is familiar with naval ratings I suppose that's not really a worry.

I'd pick Soldier to go with Sailor, but that's just me.

Captain, maybe?