Absolutely! Their entire purpose is to take over the ship and redirect its mission to something other than taking whales. You've just redefined piracy with the word protest and think that makes the activity acceptable.
Yes, I have heard the word 'protest.' It can be done, in this case, from land. A protest is strictly verbal. Once physical actions takes place, i.e. blocking access, physical confrontation, boarding ships,you have escalated past 'protest' to 'prevention' and 'provocation.'
It’d be fun to turn the tables and Japan Self Defense Force commandos board the Sea Shepherd mothership, arrest Captain Cocoapuffs himself for piracy on the high seas and convey his @ss to Tokyo for trial.
Any Law of the Sea scholars out there?