Let's stick to this hemisphere. It will make this answer a little greener, because if you're flying half-way around the globe you've already belched enough greenhouse gases into the air that it hardly matters if you stay at an eco-lodge or some golf resort made of elephant tusks on the bulldozed site of a former rainforest.
So the answer is Costa Rica, which has been leading the green travel movement for more than a decade. It can brag more than 68 eco-tourist operations certified by one of a handful of environmental accreditation groups. Second is Guatemala, with 39. The United States is third at 38. To see the full list, check out the Rainforest Alliance's "Go Green! A SmartGuide to Sustainable Travel in the Americas."
The numbers are growing every year, as more people realize they don't necessarily have to give up 1,000 thread count cotton linens and personal waiters serving them frilly drinks on the beach for the sake of eco-friendliness. I've been to a handful of different green resorts, but the one I'd most like to visit (and haven't) is Tiamo Resorts on South Andros Island in the Bahamas. It's undergoing renovations to its 11 beachside bungalows right now and will open again in October. Tiamo is powered completely by solar panels, it's surrounded by a 125-acre preserve, and it's built by local construction crews who cleared and carried the lumber for it on site by hand.