I would personally fly into Heraklion because there is a lot to do in that area. You can always make your way to Chania later on the trip. Since Heraklion is the larger airport, there ear more options for flights.
I swear Greece is one of the only places where visiting monasteries is like a must do! Toplou monastery is so stunning and I highly recommend it for anyone who wants to see some less touristy sites in Greece!