yes, go to a site like Expedia, Travelocity, or Kayak and look for flights to where you want to go. When you find a flight you like, check the individual airline site too to make sure they don't have a better deal on the same flight. Some destinations may be serviced by a regional airline that isn't covered by the US travel sites. Usually the website for that airport or a local tourism website will have a page that tells you all the airlines that fly there, so if they say Joe's air flies there and none of the major US sites are showing you flights from Joe's air, you will need to look into that directly through the airline or maybe a travel agent. (Whether or not you want to fly Joe's air is a separate issue.)
Most dive package deals don't include flights because people can be coming from anywhere, though some of those places will also arrange flights. Sometimes you can find hotel/flight deals that are good because they use charter flights and they're basically a locally marketed thing, but they're for the general public - even if they are to a dive destination they they probably aren't going to include diving. And you can find lots of hotel/flight deals on the travel sites I mentioned, but in some destinations they don't cover the hotels you are most likely to want to stay at as a diver.
You could also use a dive travel agent to book the whole thing. It shouldn't cost you any more than doing it on your own, though you'd want to be aware of any deals available and make sure. Sometimes a good deal might not be offered by an agent because they aren't paying a commission on it. Sometimes an agent can get you a better deal than you can yourself, especially on air, though that seems more likely in the Pacific region than the Caribbean. There are threads around here where people have discussed good dive travel agents.
Does any one have suggestions for going to USVI, BVI, Cozumel, Curacao, Keys, or Honduras?
