You can reach Chania by airplane or by ferry:
The Chania International Airport, "Ioannis Daskalogiannis" (IATA code: CHQ), is located on the peninsula of Akrotiri, 15km from the city of Chania. It hosts domestic flights to and from Athens and Thessaloniki with Aegean Airlines and Olympic Air (members of Star Alliance). During the high season (April to early November) there are several direct flights from many cities across Europe with Ryaniar, Easyjet, as well as charter flights.
There is public transportation connecting the Chania International Airport with the city center. The schedule can be found here.
You can reach Chania from Piraeus port (located 50km from Athens International Airport "Eleftherios Venizelos") to Souda Port of Chania with Anek Lines. A regular bus service (buses leave every 20 min) connects the Souda port to Chania city.
Transfer by taxi is available at a cost of 25€-30€ from the Airport / Port to the city centre.
More information can be found here.