First time via Toronto (Baltimore -> Toronto -> Havana).
Second time we took one of they very few available IIRC American Airlines flights from Miami. Baltimore -> Miami -> Havana.
Believe it or not, the Canada trip was much easier. In Miami we encountered a lot of hostility from the Miami Cuban immigrant community. Eg, the gate to fly to Havana was really hidden in an obscure place between two terminals, and we felt people were jerking us around when we asked how to find it (we were literally sent to both extreme ends of the airport a couple times). Returning we had some aggressive questions from an immigrations officer when he found out we weren't visiting family there, and sent us to the line for getting our bags fully inspected for farming produce contraband.
So yeah, it is possible to fly there from the USA legally, but in our opinion flying waaaay out of the way to Canada was actually easier and less stressful.