My heavens Lizcat, the Blue Star ferries carry from 1400 - 1800 passengers, and 250-300 vehicles, they are not like bay ferries like those in Seattle, or Staten Island etc ... they are more like small ocean liners. In June Ive never seen the inside reserved seat areas (called "aircraft seating") more than 1/2 full, and I've done numerous Blue Star journeys in May & June on 12 trips to Greece. I would see no need to buy passenger tickets more than a few days ahead, except a week ahead if you are outbound from Piraeus on the 5:30 Friday boat on the early-summer "Holy Spirit" (pentecost) 3-day weekend -- only this year its may 25-28 anyway.
Can't answer about Aktina airport purchase, because It's fairly new there, I bought tickets from its predecessor agency without incident. One thing that used to be true, don't know how true it is now ... if you bought reserved-economy tickets online you could not specify location, only if you bought at agency or at the Blue Star dock office. And if you are ARE taking ferry to Santorini, a loooong journey (7:30 am - 3 pm !!) location would be important. You'd want to specify a SIDE compartment seat. The central area is like a big movie theatre, maybe 500+ seats, divided by 2 isles, noisy brightly lit, overhead TVs on constantly. SIDE compartments (used to be nonsmoking - now there's NO inside smoking) , they are quieter, smaller 2-3 seats per side of 1 aisle.
The ferry from Santorini to Naxos is a nice 2-hour ride, fun to just sit out on deck the whole time. But from Piraeus- Santorini?? Reallly? there's nothing to see after the first 20 minutes and you lose an entire day -- and reserved-seat would cost ?? €60+? If you can still get a fllight I would consider it -- 50 minutes. If you take the "early bird" departure (6 am or so), there may still be some seats, and a decent price.