There are daily flights from Athens airport by Olympic Air, Aegean Airlines and Athens Airways (Which take about 45min.) to Heraklion and Chania. Sky Express operates flights from Athens airport to Sitia. During the months of July and August Astra Airlines flies from Thessaloniki to Heraklion and Chania.
From April until early November charter airlines fly directly to Heraklion and Chania from many European airports.
The airport at Heraklion also has daily flights to Rhodes which takes 1 hr. There are daily flights between Athens and Heraklion.
Crete has many ferry connections. You can go from:
Pireaus to Heraklion with Minoan Lines
Pireaus to Chania with ANEK Lines or Hellenic Seaways
Pireaus to Ayios Nikolaos and Sitia with LANE Lines.
LANE also operates routes from Ayios Nikolaos/Sitia to Rhodes and other greek islands.
In the summer, there are daily catmarans (hydrofoils) from Heraklion to Santorini. The trip takes about 2.5 hours. Hellenic Seaways and SeaJets offer these sailings. Y
You can also go to Crete by ferry from the Peloponnese (Gytheio) and Kythira island. This ferry lands on the west part of Crete, in Kissamos port.
The main ports in Greece that ferries come into are in Heraklion, Chania, Rethymno, Sitia, and Kastelli-Kassamos.
For more information see Greece, Getting There