Unless he had a brace and auger with a bit three feet in diameter. Three holes, or nine holes, depending on whichever version, ought to do the trick, I would think.

A couple of things I've wondered about:--
1) Did he have to swim alongside the enemy ship while it was under full sail while doing the deed? Or was the ship just sitting there like a swan on a smooth pond?   
2) Even if it were just sitting there and all he had to do was tread water, the trick would be to set the auger bit into the wood of the hull and apply enough pressure to screw it through the planking without pushing himself away from the ship.

Tricky piece of work.

Astronauts working in space have to brace themselves against something when using rotary tools (such as an electric drill or screwdriver) or they find they push themselves away from what they're working on when they try to apply the necessary pressure and counter-rotating when they operate the tool. In a medium that doesn't offer very much firm support such as water, it seems the same problem in physics might pertain. Newton strikes again!

Don Firth