Personally, I would go as late as possible because if you miss the connection the responsibility is all yours. It doesn't take too much for your inbound flight to be delayed and I've had one terrible experience at ATH in reverse - a flight from Mykonos to Athens, collect bags then check in to a Schengen flight - although I had hours - getting my bags meant I made it with seconds to spare.

As as guide (assuming you have luggage) you will need to deboard, immigration to Europe, collect your bags, check in for your Santorini flight, security and usual waiting times.