The best thing to do is to find out about the buses from the Athina Palace, and that way you can visit not only Heraklion but also Aghia Pelaghia. By going up to the busstop on the highway you can intercept the bus to Rethymnon too. The historical museum is really good, and so is the Fort in Heraklion. The Sirocco restaurant over the hill in the next bay of Ligaria is fantastic and very good value. Try the moussaka!