Wouldn't the old grappling hooks and climbing up the side work? I can't see a whaling ship being particularly nimble or nippy. Pull up alongside, and climb onboard. Once onboard, try to vandalise the board, get beaten up, strapped to the mast while they clear a room to be used as a cell, and then thrown in.
Edit story above depending on which side is telling.
"We pulled up beside the boat, got onboard, and then got assaulted, and tied to the radio mast!"
"They boarded the boat without permission via grapples, and attempted to tear down the radar mast. So we restrained them while we were organising a containment area for them."
Depends on who you listen to.
Actually, just read another news article.
"The two boarded the Yushin Maru No 2 after they made attempts to entangle the screw of the vessel using ropes and throwing bottles of acid on to the decks."
But Watson said as the two boarded Yushin Maru the Japanese attacked them.
So, no provocation other than trying to damage the ship then...