Naxos to Athens

We flew. After taking a rather rocky ride from Santorini where my daughter got sick, we were very glad we did.

We also flew. It all depends on what you want to do.

It's a personal choice, but we flew Aegean.

while there is something very Greek about the thought of island hopping by ferry you have to realize that route will take about 5 hours. If you fly you will be in Athens in less than an hour. If you take the first flight of the day you will be in Athens in the morning.
We always fly. It may cost a bit more but its worth it.

There's no predefined "best" or "worst."

The "best" could be the one that fits the context and your preferences.

It depends on how much time you have and how long you are willing to take to get there. And what you are doing next. We flew from Naxos to Athens, and that worked our very well for us. it's a short flight. About 40 minutes, I think. Then we picked up our rental car at the airport and drove to Nafplio. Unless I had a lot of time, I would fly.