You can find timetables for Greek ferries here: https://www.greekferries.gr It's also possible to check which companies are operating these ferries. You can travel with the Greek Islands Pass using Blue Star Ferries and Hellenic Seaways, which cover most Greek islands. Check out this document for all the information: https://www.interrail.eu/content/dam/pdfs/greek-islands-pass-guide.pdf
As a general rule, all islands withing an island group are interconnected. On top of that, most islands have connections with Piraeus, near Athens. Connections between island groups is often done using hubs, like Paros and Samos.
As for your route: this is certainly possible. Between Mykonos and Santorini you might need to change in Naxos or Paros. From Santorini there are direct ferries to Heraklion, Crete, however I'm not sure which company it operates. (note: in case you need more than one ferry on a travel day, you can use the same travel day)