Yep they are, and there are some Greenpeace pirates in Japan currently on trial for that.
I think you are referring to Pete Bethune, of the Sea Shepherds. He has already pled guilty to three charges for boarding a Japanese whaling ship. Paul Watson, the founder of the Sea Shepherds, was an early member of Greenpeace but was ejected from the organization. In fact, Greenpeace doesn't want to be seen near the Sea Shepherds at all.