Here's one website with information on ships in port: Cruise TT. There are others (just Google "cruise ships in port"), and it would probably be a good idea to check multiple sources, since this factor can seriously affect your enjoyment of some coastal cities.
You need to get a guidebook that covers Slovenia and especially Croatia, to help you winnow the list of possible destinations down to something more manageable. A good guidebook targeting budget or mid-market travelers (i.e., those who may not necessarily use rental cars and taxis all the time) will provide useful information on transportation links that will help you determine what is likely to be feasible in a given amount of time. Then you can look further for more details and more current information.
I don't have recent experience visiting any Croatian islands, but here are two online resources that can help with logistics:
Rome2Rio.com is a good first step toward determining whether there is bus service and/or ferry service and very roughly how long it might take to move from Point A to Point B. The information is not terribly precise (don't trust the prices!), but if you keep drilling down, you will usually eventually arrive at a link to the website of the appropriate bus or ferry company, where you may find schedule information. If not, Google "ferry Split to Hvar", etc.
BusCroatia.com is a rather comprehensive source for information on inter-city buses, including some that connect to Slovenia (of which there are not many). However, it is essential to verify the information once you reach Croatia. I always tried to stop by the local bus station a day or two ahead of time to look at the posted schedules, though I found the local tourist offices quite helpful if they were terribly busy at the time (could be an issue in Dubrovnik). This is especially important for buses that cross international borders, which you should book ahead of time since they sometimes sell out. The young people in both Croatia and Slovenia tend to speak English quite well, so it probably won't be as difficult to confirm schedule details as you might imagine. Do not, however, expect to get detailed information on Croatian buses while you are in Slovenia, or vice versa.
Bus schedules often vary more by day of week than from month to month, so if you find limited information available at this point for next summer, check the schedule for the day of the week you expect to be traveling, but use a date in December. Sunday schedules--which often apply to holidays as well--can be quite limited, so that's a good day to plan to explore the city you're currently staying in. And of course do investigate the holiday calendar for both countries.
It has been mentioned on this forum that lodgings on the Croatian islands often require at least a three-night stay, at least during the busy season. I don't know whether you'll run into that during your anticipated travel period. You could do some preliminary checking (trying 1-night bookings vs. 3-night bookings) on booking.com, to see whether many more options show up for the longer stays.
I'll close with my usual warning about Plitvice Lakes National Park: This is one of Europe's top sights, but everyone knows it, so it is slammed with thousands of tourists every peak-season day in the same way Dubrovnik is. And the walkways in the park are a heckuva lot narrower than the streets in Dubrovnik. To have a really enjoyable time at Plitvice, you must spend the night before your visit very near the park and get an early start the next morning. Others have found that it can be nice to visit the park very late in the afternoon as well, after all the day-trippers have left. Do not try to do this as a day-trip from Split or Zagreb! One night at the park should be sufficient.