Eco-tourism is still in its infancy in Cuba. Boca de Guama in the Peninsula de Zapata, close to Bay of Pigs on the south coast, is a vast wetland of mangroves and swamps, home to many species, including the stately manatee sea-cow, sadly rarely sighted. Many migratory birds also over-winter in the marshes. Boca de Guama is the main centre, about 2-3 hours drive from Havana (around $100 by taxi). There is a crocodile farm, which may or may not be considered eco, and you will be offered crocodile steaks. The upside is that the wild ones are no-longer hunted and have made a come-back. The nearby Laguna del Tesoro is accessible by boat. Here you will find a tourist resort called Villa Guama built to resemble an Arawak village the Arawaks were the indigenous Indians largely wiped out by the Spaniards.
The resort consists of huts built on swamp islands, but don't count on seeing too much wildlife. There is a noisy disco, the place is overpriced and tacky and the boatmen have a habit of picking you rare water-lillies on the way over in the hope of a tip.
The spectacular Gran Parque Nacional Sierra Maestra is at the eastern end of Cuba (from Havana 16-20 hours by train or bus and about 18 hours by taxi expect to pay $300-400 and make the journey in two or three legs). This was Fidel Castro and Che Guevara's base during the revolutionary war of 1956-9. The park also contains Cuba's highest peak, Pico Turquino (1972 m).
There is basic tourist accommodation in the park. The main base is Villa Santa Domingo near the town of Bartolome Maso which rents cabanas for around $30. Or you can stay in the provincial capital of Bayamo 40 kms to the north, a pleasant, sleepy town with some not very good tourist hotels, but plenty of good casa particulars.
There's plenty of riding and trekking and some marked trails in the park. You'll need local guides where trails are not marked. The area is wild, you will need to take food and it can get very cold and wet. An alternative way to attack the area is from the beautiful south coast around Chivorico and El Uvero in neighbouring Sanitago de Cuba province. See Cuba's must-sees.
The flat Peninsula Guanahacabibes in Pinar del Rio province in the far south west of Cuba, around 3-4 hours from Havana by car (about $140 by cab), is a UNESCO biosphere reserve good for bird watching. There are, apparently, parrots. You have to pay $10 to get into the reserve and there is a basic hotel at the rocky beach resort of Maria la Gorda where the diving is also excellent see Dive Cuba.