Marinas in
Cuba are available in both Cayo Largo and Cienfuegos.
After spending time at both I think they are safe and there are people that could watch your
boat.
Cienfuegos would be easier for you to get to the Havana
Airport if you wanted to rent a minibus or car. However you could also fly out of Cayo Largo to Havana if
money is not an issue.
However my suggestion would be to leave the
boat in Grand Cayman (overnight sail to Cuba) either at a marina or Private
dock which most are in gated communities and quite safe. Also quite reasonable prices compared to the
eastern Caribbean and you can get most anything you need there.
I should mention that Port Antonio
Jamaica has a very nice marina and they are really trying to grow. The boat boys that walk the docks are a bit irritating but I think your boat would be safe. Also the airports are quite a distance with Kingston being the closest.
Good luck on your voyage.