I disagree, for several reasons. I believe that 2 1/2 hours will be plenty. Do you recall the time of year you went before? And the day of the week? The incoming traffic is greatest on Saturday, and bigger crowds at very end of June through late August.
There is no "customs" to go through... what you are talking about is the passport control line.... that's the only thing that will take any time. If you are worried, then do your best to choose seats that are towrds the FRONT of the economy section of the plane. Then get your 2 teens to wrangle their bags from the overhead and HUSTLE towards the passport control line, to be near the front, then you join them there. The maximum amount of time for the line should be no more than 45 minutes at most, and no time waiting at the bag carousel, which often takes more time than the above. You do not have to switch to another building, just go to other side of same building.... and you just need to be in the domestic check-in line 45 minutes before departure. Back in the day, you had to pick up your Aegean/Olympic tickets at their counter before getting in the check-in line, but I believe that's finally been modernized since 10 years ago... check their website to be sure.