It is hard to advise when you are so terse with details. What TIME of day do you arrive on Thurs May 2?? Unless you arrive after 6 pm you should FLY (allow a 2 hr layover) immediately to SANTORINI. A ferry takes 8-9 hours (and most of the trip, nothing to see but sea), a flight takes 50 minutes -- and in Early May, depending on time of day, the $$ may be roughly the same. If you arrive 6 or later, I advise staying near airport (but on a beach) at Hotel AVRA ...recently renovated v. nicely -- a 25 min ride on FREE Shuttle to/from airport -- and take early AM flight to Santorini.
• SANTORINI - going on Thurs night would give you 3 full days/4 nights there... so I would say leave Monday AM on ChampionJet 10:30 or so, for NAXOS - open back deck permits nice departure view & photos, arrives Naxos by noon.
• NAXOS - I propose you devote 4 nights to Naxos, and skip a stay in Mykonos. Naxos is a super island for scenery, antiquities, walks, drives, food, nightlife... not yet totally touricized so spend time there before this changes. If Mykonos is a "must-see" there's a daily excursion from Naxos (which also has option of 3 hours on the sacred isle of Delos). Since you will have already seen one v. expensive, totally touristic Greek isle (plus the Famous Caldera View), why see another... if you've been to NYC or Palm Beach or Beverly Hills, you already have been to "famous name" luxury shops Cartier-Hermes-Calvin-Boss-DKNY etc etc, no need to re-visit. Friends say "you must see Mykonos" that's because they were there on a cruise.
• RETURN to MAINLAND -- Flight or Ferry? Again, options. Flight = 45 mins vs. 5.5-6 hours. If you DO decide on Ferry, I suggest the Blue Star departure 6pm - 11:45pm ... Enjoy sunset on deck, get "reserved economy" seats for sitting inside later, large comfy leanback seats to read,snack, snooze. That way u dont have ferry ride 9:45 - 3pm using up most of a day.