You take the subway-green line to Pireus.The train have schedules every 3minutes from 05.30am-24.00.
The duration from Omonia square to Pireus port is 20minutes. Ticket price is 1,20€ and you buy it at the stations.
Opposite the train station in Pireus are the gates E6-E7. From these gates are leaving all the boats to Cyclades Islands.
All the other gates are located nearby.
You must be at the boat 30minutes before departure.
Have a nice trip.