"If your goal is to avoid all-inclusive resorts and engage in something more akin to "travel" than to "tourism," then you should consider the offerings by the multitude of US tour companies that operate in Cuba... these companies typically handle flights, compliance with US travel restriction to Cuba, visas, transportation and programs that get you inserted into the culture and environment that would be difficult to do by yourself...
In the news
"Cuba Unbound has something new to offer travelers heading to Cuba: kayaking and walking tours on the wild, east end of the island. People-to-people trips start in November for an experience that organizers describe as a “little more raw” than the usual island-nation visit."
Canoe & Kayak
"Imagine paddling off the coast of an island in the Pacific Ocean. To your right is a long, sandy beach with a bare volcano rising behind it. To your left lies endless ocean dotted with more small islands. A light breeze blows across the water. A sea turtle pops its head up next to your boat for a breath. A few minutes later, a dolphin jumps in the air just yards from the bow of your kayak. You paddle by a bait ball of sardines and a hammerhead shark rips past you, splitting the school of fish in two.
"Time stops in British Columbia’s Inside Passage: Stretching from the northwestern edge of Washington State and extending into southeast Alaska, this coastal route weaves through thick wilderness where a day at sea includes roaming free with humpback whales and orcas. Towering trees stand erect against the haze of ambient cloud streams, and you can feel a steady, internal shift accruing, cementing a lineal connection to nature this landscape provides...."