This is just my opinion. I can understand why anti-whalers want to protect the species. They are some of the most beautiful creatures in the ocean. Also, the oceans are a public good, which is very prone to overuse. Because no one "owns" it, the normal tendency is a race to fish as much as possible before someone else does. So without the anti-whalers, there is a very good possibility the ocean would be over fished (or whaled as the case may be), which would be a tragedy.
That being said, I think the Sea Shepards harm their cause more than help it. First, this show has shown the "fantasy" world they operate in. Just one example, they send over two crew mates (with overnight bags) and refuse to take them back, then claim that they were kidnapped. That stunt convinces me that they would be perfectly willing to stage a fake shooting. The captain has no regard for anyone else other than him (and only some little regard for a few that think like him).
In the real world, you can't just have your way with everything, just because you think you are right. For example, this whole idea that what the Japanese is doing is illegal. It clearly is not. The Japanese, a sovereign nation, bound itself to an international treaty. That treaty bans most commercial whaling except for a small quota that they label "scientific research." It doesn't matter what the label is... they could call it Star Wars fishing, the fact is that they are allowed to whale for a certain amount of whales every year. Now, the sea shepards claims that they are fishing in a sanctuary. Yes, Australia declared that area a sanctuary. However, Australia does not have the authority to declare those waters off limits to Japan. The sanctuary ruling only applies to Australian citizens, not to other nations. The claim that what the Japanese are doing is illegal is, just like with most things the Sea Shepards claim, a twisting of the truth for PR. (Though, I don't deny that the "scientific research" is mostly just a PR way of allowing some commercial fishing.)
So, the point of all of this, is that they only way they are going to stop Japanese whaling is to convince the Japanese to give it up themselves. There is no way they are going to convince the Japanese to submit to Australian law. Frankly, the Japanese were duped into signing the treaty anyway, by incentives from the US that we reneged on.
So in the end, Greenpeace has it right. Run a public info campaign in Japan and get enough citizens there to demand a stop, and they will reach their goal. What the Sea Shepard do seems for their own benefit. And it just hardens their opposition's opinions. They come across as so unreasonable that some of their actions during the season, must have set back their cause by years. They are too focused on the means and are sacrificing the ends.
I started to watch this show mostly because I like the Deadliest Catch. I kept watching it for the comedy of they silly people pretending to be sailors. I'll keep watching because it is entertaining. However, as far as agreeing with them, I just can't. They are just too unreasonable.
Like I said, just my opinion.