Hire a driver in Crete

It depends on how much time you want to spend at each and how much you want to spend. All are in a relatively compact zone and accessible by city bus. I can't exactly recall, but certainly you can get a taxi from the port to Knossos, and I assume Knossos probably has taxis nearby on exit, the same with the museum. My point being, you may just be able to use a taxi when you need it, rather than pay a driver to wait. If all else fails, you can hint that you may need a taxi on exit from Knossos, and likely someone will be there (or set up a time). Since the museum is in the city, a taxi from there to the port should not be a problem.

I visited Crete few years ago, I loved it! I remember that public transportation was very accessible to both the places you mentioned. Indeed, Heraklion is like a 'big' city and taxis were every where. Loved the taxi drivers in Greece in general, they are too dramatic and funny at the same time. happy travels.