There are many variants of this question asked/answered in various sections of the
forum.
Since it appears that you are booking two separate tickets, one to Athens and one to Crete or Paros,
you will, if you check luggage, have to clear customs in Athens and then reclaim your luggage, and
recheck it with the second airline (even if it is the same airline) to the final destination, and then clear
security again.
It's possible that the originating airline could be nice and tag your bag all the way to the final destination,
but you can't count on it.
If you just have carryon, you still will clear immigration in Athens but I presume can transfer to the
next flight without having to exit secure area/claim luggage.
The second part of this is the risk you are willing to shoulder for possible delays on your inbound
flight. If your inbound is delayed and you miss the connecting flight (assuming it's a separate
ticket), then you are not protected in any way and at the mercy of the second airline. You could end
up being stuck in Athens for a while.
Athens is not that large an airport, so if everything goes right, including you not making any wrong
turns, figuring out where everything is, etc, it should not be that bad. But I am not going to suggest
a specific amount of time, and I think most folks here would say it is much more prudent to spend a
night in Athens to avoid the possibility of a much larger screwup.