At this point, it will still be cheaper and easier to fly from Canada. Flights from the US are still charters and require licensing and are fairly expensive (not to mention not available to non citizens/permanent residents).
A good site to use is Sunwing.ca (not to mention they as they buy a lot of rooms) offer some split package (typically X nights in Varadero + Y nights in Havana). I found hotel offerings in Havana to be somewhat dismal especially if you want to stay in Havana Vieja.
Sunwing flights are more limited however. Westjet has more "scheduled" service.
What you could also do is book into a casa particulare in Havana and resort through the vacation sites (they sell off surplus inventory). Retail hotel rates (i.e., what is charged to the independent tourist who arranges on their own) is ridiculosly expensive.
You should be o.k. going to Cuba and re-entering the U.S. if you are not considered a U.S. person.