It is great that we can start to plan for Greece next year.
When are you planning on going?
We too fly from the west coast (what a long haul, 24 hours of actual travel time). Never the less whenever possible we get out to our first island on the day we arrive in Greece.
Santorini is very popular so there are lots of flights including late night arrivals so we would finish the trip by flying Athens to Santorini on day of arrival. Waking up on an island is way better than waking up in Athens after a transatlantic.
Just another thought. If your flight goes to another European destination first where you have to connect for Greece ,you might want to see if there are direct flights to Santorini from your arrival location. For instance we have a direct flight to Munich where we change planes and fly into Athens. Check to see if there is a direct flight to Santorini instead.
While Mykonos is lovely it has chosen to brand itself as a high end destination which means very expensive. Naxos has everything and more than Mykonos but at half the price. Good choice you won't regret it.
Your number of days is good. Three nights is all my budget can withstand in Santorini. 4 nights Naxos is good, a week would be better. Any chance you can coax a few extra days for your vacation?
Do fly back to Athens. Three days is a decent amount of time there but in a pinch you can do the main highlights in 2 days.
Here is why Naxos is a good choice.
Naxos town https://www.flickr.com/photos/stanbr54/albums/72157632094558042
Trip around Naxos https://www.flickr.com/photos/stanbr54/albums/72157634605629689
Naxos 2017 https://www.flickr.com/photos/stanbr54/albums/72157663620712358
Naxos 2019 https://www.flickr.com/photos/stanbr54/albums/72157711294807761
Have fun planning.