Probably the easiest is to book a flight to Cancun and then fly to Habana from there. Even with permmission it will be a lot easier then flying offically through the USA. A friend who has a had a permit for Cuban travel has done this many times and vowed never to to fly offically through Miami again.

The alternative is to fly to the Carribean such as to the Cayman Islands and then fly a Cuban airline from there. However, your trip will begin before you get to Cuba . If you go that route note that window seats are limited and smoking is restricted except in the cockpit.