2nd vote for Ban Tours
I know this is an old thread, but I found it earlier this year while looking for recommended charter companies in Croatia, and I want to echo PCP's recommendation.
We booked a Dufour 455 with Ban Tours out of Rogoznica and couldn't have been more pleased with the experience. They're a small but growing outfit with a fleet of 15 Dufours from 11-15m, and they own the boats. Our boat was impeccably maintained and the staff very friendly and helpful. The service felt very personal.
I would also add that Croatia is a fantastic destination for a 2-week charter, and that the islands, anchorages and marinas are plentiful enough that itineraries are best planned as the wind blows. We rarely knew where we would be more than a day or two in advance. Our route was much like Maxivalt's first suggestion, hopping from island to island sailing to and from Dubrovnik over two weeks. It was a memorable trip.