What is the best option to get from Cuba to Costa Rica?
As usual, 'best' is not a good question? Does that mean 'cheapest', 'fastest' or 'best scenery'?
It seems there is only one direct flight from Havana to San Jose, this is with TACA Airlines, a one way fare can be found for $350 US.
Alternatively you can fly to Cancun (Mexico), Managua (Nicaragua) or Panama City and then take a bus.