The thing I think might have been missed to this point is that if the anti-whaling forces are willing to abandon non-lethal methods, shoals of small, fast vessels could swarm whalers easily and anti-ship missiles - even the heavier models - are surprisingly compact and light-weight.
Forget that. Eco-terrorist cells wouldn't have access to expensive, high-profile gear - think old fishing boats and secondhand Zodiacs. Improvized weaponry, matrix assaults, and magic are likely to be the name of the game.
Anti-whaling groups are likely to have amongst their numbers a large number of "avenger"-type toxic shamans. This neatly solves both the issues of firepower and reconnaisance. Considering that they could probably aspect the boat they're travelling on in their favor, a couple of initiated toxics could easily sink a small whaling ship.