There is a shuttle from the cruise to the city Chania, 1.5 euros. Chania is a very nice city, with a Venezian flavour. Nice to walk around and sit down to drink something. We wanted to go to the Balos Lagoon, close to Kissamos. You can take the bus to Kissamos for 4.4 euros and then rent a motorbike or car to the parking lot close to the lagoon, then walk down for 30 min. At the end we did not make it to the lagoon. We arrived to Kissamos and went to the port. Then walk along the coast and you can find two great little beaches with pristine water and not tourist around.
From the cruise you walk 40 min to the subway station, then follow the lines to Acropolis. 1.4 euros ride. There were private buses too, but we did not use them. Go to Acropolis and the museum (12 and 5 euros, student discount is available). Great experience.
The best port of all. Take the cable car up, 4 euros each. Otherwise be ready for walking up hill 400 steps, covered with lots of donkey poop. We took the hike from Fira to Oia (look it up), breathtaking views!! Both from the sea and the city. Grab a bite looking at the sea from the heights
We did not expect it to be so nice. Little little town. There is a "fun train", hop on/off. 6 euros, takes you to the Mercuri Winery and to the beach. The Winery is highly recommended. Beach is nice...we did not go to Olympia. You could go taking an hr train and walk around the ruins...