If you want to visit these sites it is a taxi or an organised trip, it is a long journey and you will need to be up and out early. It is an ambitious trip for a cruiser and though public buses run every hour and take 2.5hours to get there from Chania, the saved half an hour you might get by a coach or taxi gives you more time there. Take packed lunch as you won’t want to waste time eating out. If you choose taxi or public bus, you should also find a local guide. If you take a trip you will be taken from the ship and brought back in good time. You will head to Heraklion reaching the city hopefully in 2 hours. It can take almost three hours. On the way to Heraklion you make a stop near Rethymnon for a few minutes, though this may be worth leaving for the way back in case time is short.
The first real stop is the Palace of Knossos, a complex of more than 1500 interlocking rooms. Built in the Bronze age (2000 BC), the palace of Knossos is considered Europe’s oldest city and is referred to as the centre of Minoan civilisation. The people as well as the palace was destroyed by the eruption of the Santorini Volcano (1700 BC). A new palace was built with many splendid frescoes adorning the walls, hundreds of rooms and workshops distributed in four storeys with spacious courts for hosting ceremonies and feasts. But further earthquakes in the 14th century BC led to the final destruction. Excavation of the site was between 1900-1930 and many of the results are at the museum. This alone is a licensed guided tour that takes an hour so you can see the time vanishing.
Next is the centre of Heraklion, where there is much hustle and bustle as well as a chance to visit the archaeological museum of Heraklion. You have come this far so it is worth the licensed guide to explain the artefacts and murals and as well as repeat some description of the palace you have just visited.