Boston to Naxos via Athens - checked luggage, EU Passports - 3hr layover enough?

Is this on one ticket or two separate ones?

If one ticket, you will go through passport control in Athens, your bag should automatically be transferred to your flight to Naxos, and you will go through customs in Naxos.

If two separate tickets, you are risking having to buy a new ticket--3 new tickets--if your flight is delayed into Athens.

If one ticket, you will go through passport control in Athens, your bag should automatically be transferred to your flight to Naxos, and you will go through customs in Naxos.

There is no customs facility in Naxos. Only EU-originated bags (exempt from customs) can be checked through to Naxos. Everybody else has to reclaim their bags in Athens and recheck them even if travelling on one ticket. Note it's where the bag was checked in that counts, not the passport. EU passports are irrelevant for this purpose if flying from Boston.

3 hrs is normally OK.

In Europe, customs is nothing. You walk through a door and it take about 5 seconds.

Sounds like you need to worried about passport control and the time it will take to claim your bags.

Can we assume that you are on a direct flight from Boston to Athens? If the answer is yes, then you will go through passport control in Athens. That could take time. If the answer is no, then were are you transiting?

As for the time at baggage claim, I'm sure others have more recent experience, but this might be a good argument for taking only carry-on luggage with you.

I'd be most worried that you flight into Athens will be delayed.

Athens is not a huge airport. 3 hours is plenty. We did passport control, got our bags, went through customs, and were out of the airport and on our train in less than an hour. The one factor you have to add is (perhaps) getting your bags (which is usually outside security) and then having the pass through security again to get to your gate. Some airports handle such connections better than others. I still think you'll have plenty of time.

Family of 3 flying (EU passports) from Boston to Naxos and connecting through Athens on a different ticket.

From your statement it appears that you are flying on separate tickets. Please confirm.

I've been through ATH on the way to the islands many times. 3 hours is plenty of time.

Three hours is lots of time to make the connection. Generally 2 hours is about right. Here is what you will experience. Arrive Athens many of the tranatlantic flights arrive between 10am and 1 pm and the airport is less crowded that the early morning.
Both Sky express and Olympic/Aegean fly into Naxos. They both allow you to print your boarding passes 48 hours before your flight time so you will have your boarding pass before you leave home.
You will have to go through passport control. That can take up to 30 minutes if 4 jumbo jets all arrive at the same time.
After passport control you will pick up you bags and go out the exit door. That door says nothing to declare. That was customs. Go up one floor by stairs elevator or escalator. You are now in departure level . You will need to check your bags ion the Naxos flight. You can do that at the airline counter or you can print luggage tags and drop off your luggage onto a conveyor machine.
Now go to security. Athens airport has one of the fastest security checks.
By the way Naxos is a great destination. Where are you planning to stay.

Just to answer some questions:

We are flying from Boston to Athens via Delta. We are flying from Athens to Naxos on Aegean. These are booked as separate tickets so we will need to get our bags and re-check them. We have EU passports.

I double-checked the flight history of the BOS to Athens leg and it's mostly on time but a couple times it would only give us a 2.5hr window. Knowing this, we're going to book the flight after which will give us a 5hr layover window. I hate waiting around in airports but hopefully the Athens airport is nice.

As Stanbr and Brotherlee have tried to reassure you, 2 hours is customarily ample time ... I'm anotther that has done this at least 8 times nonstop to Greece, always on time or even early. One factor ion the excellent on-time record of nonstop flights from N. America, by the 4 or 5 airlines that run them, is this: Even if there is delay take-off, the plane has that long long long stretch over the Atlantic to make it up-- and also the globe's eastward wind-tendency to push it along.

Just to follow up on Janets advice, we were on a transatlantic flight to Greece and a passenger took ill just before take off. We were delayed over an hour before take off and we still arrived in Athens at the scheduled time. You need 2 hours to get through the arrival process and take off on your Aegean flight. After 20 visits to Greece I can attest that you need no more than 2 hours to make your connecting flight.