I think every person has to define "best" for him or herself, as it might depend on how well the environmental organization reflects your own values and preferences. You've already started to do this by prioritizing action over lobbying, protest, and education.
Efficiency can be quantified relatively well, though, so I find Charity Navigator useful as a tool to show how much of my donation goes to actual program work as opposed to overhead costs and fundraising. That said, I think it is important to remember that some programs will have very different costs than others. For example, airdropping food for people in a remote war zone is going to involve a lot more money per meal than collecting unused restaurant or grocery store to feed people in a local shelter.
Personally, I'm not a fan of Sea Shepherd, not because they don't do some good work, but because they oppose sport fishing and eating seafood, both of which clash with some of my own beliefs and activities. My own preferences skew more toward groups like Conservation International and Trout Unlimited, because they focus on protecting entire ecosystems and/or are friendly to things I also support, like fishing. Please don't misinterpret this as any kind of attack on you or on Sea Shepherd. I can respect an institution like Sea Shepherd and respect its integrity without necessarily agreeing with it. and I'm not asserting that CI or Nature Conservancy or Trout Unlimited are objectively "better," only that it might be better for me.
The only suggestion I will make in terms of "better" is that you consider donating some of your money and (especially) time to a local organization or a local chapter of a larger organization. For example, you will almost certainly have a local Riverkeeper or other conservancy organization that focuses on your local water or environment. Supporting a local effort brings results you can see, lets you participate in interesting projects, and connects you with like minded people.
Thanks for trying to be part of the solution, whatever groups you choose to support.
