Greenpeace and Sea Shepherd are commonly confused...to the abhorrence of both!
I found a copy of Watson's autobiography last year, interesting read. He was a founding member of Greenpeace, more or less got kicked out when they refused to back up his non-peaceful anti-whaling actions. (reminds me of that song, "peace sells...but who's buying")
Since then, they are pretty much enemies...they don't see each other as different factions fighting the same war, but in opposition. They consider him an eco-terrorist. He considers them an ineffectual fund raising organization.
His reasoning for his actions are somewhat compelling: there is an international agreement to ban whaling, but there is no international navy to enforce. Every country turns a blind eye to whaling actions, so while there's a law against it, it is a free for all. So, his thinking is that these whalers are pirates, and he will take it upon himself to enforce this international whaling ban.
From there, lots of ethical and philosophical problems ... but an interesting premise. Agree or not, no question he's got cojones and incredible drive....pretty much dedicated his life to it, rightly or wrongly.