Airline connections between Central America and the Caribbean are very poor, and in most cases, non-existent. I've been to Central America twice myself in the last year, and met with a few people from that region who had to travel via Miami. Check COPA Airlines, based in Panama City. I believe they have flights to Port of Spain. For the most part, you're better off going via Miami. Certainly to Puerto Rico. American Airlines, with a base in Miami, has plenty of flights to both Central America and San Juan (and many other Caribbean destinations). The ridiculous thing is that even when you can fly direct between two points in Latin America, sometimes the price is lower via Miami. A year ago I was in Costa Rica. A few friends went to Lima, Peru, after their stay in Costa Rica. It was cheaper for them to buy a ticket via Miami to Lima, then to Lima direct from San Jose!
Of course, if you want to visit Cuba, you can rule out transiting via USA. Unfortunately, Cubana has been terminating a number of their international services recently, and I am not certain of exactly what cities they fly to in the region now. Mexico City would be my number 1 guess.
[ Edit: Edited on 17-May-2009, at 09:28 by bgl ]