Travel from the north of Croatia to Dubrovnik

I don't know if there is a boat from Istria to Dubrovnik; perhaps someone else will know. But I can suggest that you look up Krilo and Jadrolinija. They are the two main ferry and catamaran companies in Croatia, and they may go from Istria to Dubrovnik.

Perhaps you could ferry to Venice and fly home from there. Check the airfare and time from Venice.

Some options in Croatia are not available late in the year. When is it that you will be there?

We have often gotten around in Croatia on a bus. There is also a ferry from Split to Dubrovnik. The ferry shuts down in the winter.

Thank you so much for your advice! I will heading to Croatia in mid May ....

With 3 weeks you have a lot of flexibility with the order of your itinerary. Why not move Istria to earlier in your intinerary and save one of the destinations closer to Dubrovnik until near the end of your trip? For example, you could work your way north skipping Split or Korcula, visit Istria in the middle of your trip and then work your way back south stopping in Split or Korcula on the way. Your overall itinerary would be just as efficient and it would make the return to Dubrovnik much easier. Having traveled in Croatia multiple times, that's what I would do.

If you prefer to return to Dubrovnik from Istria, your best bet might be to fly from Pula to Dubrovnik. It likely requires a connection (e.g. in Zagreb), but it's still faster than the alternatives. Another option would be to visit Zagreb after Istria and then either fly directly from Zagreb to Dubrovnik (fast) or take a train/bus to Split and a bus/catamaran to Dubrovnik (much slower). Note that Krilo and Jadrolinija won't yet be operating on high-season schedules in May, but there will still be adequate options. Sounds like you would be in Split or Korcula in early June if you saved it until late in your trip, and that would make getting back to Dubrovnik even easier.

It's important to know when you will visit. Venice is well worth considering for arrival/departure.

Have you considered flying into Split instead? I cannot imagine flying into Dubrovnik would be inexpensive and/or requiring a lot of connections because it's so small. Split is a great gateway to the islands and the south and north of the country. Do you have a guide book for Croatia? I used the Rough Guide when I went. You should familiarize yourself with your transportation options. There is train service from Zagreb to Split only. South of Split, there is ample bus service...there are also ferries. I think even with 3 weeks, you shouldn't underestimate how much land you're trying to cover when including Istria and Dubrovnik - that's the extent of the entire country and it has a very long coastline. I would focus on just one or two regions instead of trying to see everything. The islands themselves could take a few days each.

You could fly one direction (see if DBV to Pula flights make you route through Zagreb, but getting from Istria to Zagreb for a flight is not terribly time consuming) or just be very selective in your planning and go north and south by combo of bus and boat.