Enough time to catch connecting flight?

Is it all on one ticket?

Emirates and Aegean do not have a codeshare agreement so you will have to pick up your luggage in Athens and check it in for Chania.
With this luggage to be picked up and re-checked, and coming from a non-Schengen area, you are at the limit of what is reasonable in terms of the time between two flights with about zero safety margin.

A delay of 30 minutes or more with your Emirates flight and you are at high risk of missing your flight to Chania.

So it's up to you.

That being said, have you checked that there are no Sky Express flights to Chania between 6:00 p.m. and 10:00 p.m.?

No, it is not on one ticket!

Then you may have a problem. Because you have to clear passport control, get your checked luggage, check in that luggage with the other airline, clear security and THEN get to your gate. Plus, being on a separate tickets, if you miss the second flight, the airline has no requirement to get you on the next flight, and would charge for a new ticket.

The good news is that ATH is a pretty small airport with just one terminal so you won't spend much time just covering distance. Still, you'll have trouble if your arriving flight is delayed. Probably too expensive now to rebook to that later evening flight on to Chania, might as well hope for the best -- which often happens, believe it or not. ;-)

Where are you sitting on the Emirates flight?

If you are toward the back of a plane that seats 300+, getting off, through passport control, to bag retrieval, to bag drop off, through security and to the gate looks like a project that requires perfection at every step to be successful.

If you are in biz class, your chances look a bit better.

As unappealing as sitting around for a 9PM flight is, it might be better to plan for it, have dinner at the airport.
The alternative is probably paying extra to get onto the 9 or 10PM flight ( if they have seats)