Note that ship docks in Aghios Nikolaos.
Lefteris Nikiforakis (www.greecetravel.com/crete/taxitours) had been recommended to us. Lefteris was already booked and arranged for one of his associates to be our driver/guide. We were disappointed in that our guide's English was not as good as we were led to believe it would be. We recommend that everyone agree on what sites to visit in advance. There was also some confusion here.
Our recommendation is to consider renting a car and driving yourself for a tour on Crete. Roads are quite good and easy to negotiate.
The Palace of Knossos is the main site to visit on Crete. Knossos is an absolute "must see". Two couples traveled together and chose to hire a private guide at the entrance to Knossos. Strongly consider doing this. It is worth the money.
Also allow time for the Archaeological Museum in Irkalion. It is under renovation and only one floor is open but some of the best items in the museum are on display.
Palace of Malia is closer to Aghios Nikolaos. However, the ruins are not in good shape and save time by skipping this site.