Well, yeah, with OTL's situation. But is there any POD with which we could get a long-running ecoterrorist group?
You would need to base it out of a country that suffers from serious issues regarding law enforcement or a partially sympathetic population (or both). Some groups like Al-Queda operate generally from countries that are poverty stricken, corrupt and divided. The chaos allows them to stay hidden as there is basically nobody there to stop them or those that can, have been bought out. Other groups like say for example the IRA, had sympathy from the local population, which allowed them to stay hidden from the British.
The problem you would find with a long-standing militant eco-terrorist group is that it would be difficult to stay hidden for long. Most eco groups are first of all, based in Western nations (Eg. Greenpeace was founded in Canada, or PETA in the US) where (not to sound cynical) they have the education and the time to worry about environmental issues. They would probably have to be based out of Western Nations (they can't really go anywhere else, because their cause wouldn't garnish local support and protection) and that is extremely difficult to maintain. Unless there was some sort of populist movement supporting this eco terrorist group, they are going to be hunted down and captured by the authorities very quickly.
Also, in all honesty, having a more militant group like the Sea Shepherds isn't really possible (at least not for long). If they attacked a Japanese whaling vessel with weapons, they would be rightfully declared pirates and dealt with accordingly by naval authorities (either arrested or finding themselves on the receiving end of a Japanese exo-set missile.)