Rent a car, its not too expensive, most places have special offers eg; rent a car for 2 days and get one day for free. You can rent a bike to see the island, but it takes more time, you won't see as much as going by car, and as most roads have holes and no lighting at night its hard to ride there. The difference in price between a bike and a car is not much.
maps of the main cities
Detailed maps of Crete
And a photo that i like
I have been in Matala so KTEL Buses is the best choice how to get to the capital of Crete :)
Ticket costs around 6 Euro and Heraklion itself has 4 Bus stations so be careful about that.