The overnight transatlantic flights get in midday. You will need 2 hours to make a transfer for your connecting flight. Aegean is a code share partner in Star alliance. You can book your trip on one ticket. In that case Aegean/Olympic has to get you on that connecting flight, so you may not need the two hours.
Fly to the furthest island first, thats Crete. For you next hop to Naxos you have 2 choices, already suggested. We have always taken the early ferry from Heraklion to Santorini which takes just over 2 hours. You can change ferries in Santorini but the one we took continued to Naxos. We got in to Naxos just after noon.
While we have never flown Crete to Athens to Naxos we did use that technique a couple of times for different island hops. It is very likely that you can take the early flight Crete to Athens and connect on the Olympic flight to Naxos. You likely will be in Naxos by 9 or 10 in the morning.
The fast ferries are fairly expensive so you might find that the Crete, Athens,Naxos flights might not cost much more that the ferry trip.
The one big thing you will be missing by flying is the stop in Santorini. Arriving and departing Santorini is a remarkable sight.