I've done this trip several times, and know which sequence is more efficient ..... depending. Why why why are people so hesitant to say where they're coming from?? Please, unless you are in some Witness Protection program, please at least say which continent. It DOES matter - for instance, if coming from UK or Europe, there may be direct flights into both Crete cities... but from N America, all the nonstops (fastest, least exhausting) go only to Athens.
I'm guessing that your dates include travel time from N America -- so IN-Greece time = April 9@ noon thru Ap23; 14.5 days.. enough time to "do" Crete, Santorini, Athens fairly well. We "old hands" usually advise to save Athens (and Mainland) for last ... getting over jetlag is more fun on an island, and you learn how Greece works, & thus are more savvy about navigating a bustling capital. Plus, its world-famous landmarks then resonate more. Most efficient transit involves arriving ATH before noon, allowing 2 hr layover, & taking 1st available flight to farthest destination. Best schedule between islands is Crete to Santorini (8 or 9 am) vs Santorini-Crete (late afternoon). Thus, I'd suggest April 9 flight to CHANIA, Then Santorini, then back to Mainland.
Itinerary? 5-6 days in Crete, (2 days in CHANIA, then car rental to go South, then NE for 2 nts/ 1 full day HERAKLION (for Knossos & Fab Herak Museum), Then AM ferry to Santorini for 3 nights 2.5 days (it's mainly about the Famous Caldera View from yr balcony). Then AM flight to ATH, book accoms close/walkable to Acropolis for last 3-4 days... If u want more athens time, trim isle time. This sequence is workable ... the only cautionary note involves Ferry. Since you've selected such early dates, the only daily ferry between Crete & Santorini is probably a Seajet Superrunner, 500-800 passenger, no open-deck, if windy can be bumpy ride (however wind is worse in Autumn); something to consider.
If coming from N America, nonstops no longer have "sales" but Olympic/Aegean and Sky Express do have promotional pricing late in year, so u might hold off - this link https://en.aegeanair.com/newsletter/?a_id=2183&related=1&session=BHtOo7mo gets u email alerts to price cuts. Good luck & have fun planning!