We have been to Venice too many times to be impartial. If you have never been, it is a must. But I think 3 days is more than enough. My recommendation would be to visit Burano (not Murano) and spend half a day just walking around. It's one of the most beautiful towns we have ever visited.
There are 3 ways to get to Thera from the port. Ride the donkeys (really mules), take the cable car or take the boat around to the other side. The wives rode the beasts (they thought it was ok, and didn't smell as bad as they thought it would) and the guys took the cable care. Price is the same, 5 Euros. We walked around Thera for a while, then took the city bus to Oia. This is the city with the blue domes and the amazing sunset. It was the highlight of the trip. This was the only ship we could find that gave us time after dark to do this. Total cost of our "excursion" was about 15 Euros per person, plus snacks. This is a must do!
The ship docks in Piraeus, so if you don't do an excursion I would recommend hiring a guide since it can be confusing getting into the city and then finding everything you want to do. We used George's Taxi again, and were very satisfied with the cost and the tour. Taxigreece.com There are other companies available who also get good reviews. The Acropolis is a must and the new museum in Athens is amazing. We spent the entire day doing both and totally enjoyed the visit.
This was the most pleasant surprise of the cruise. The entrance and exit into the fjord makes it mandatory to be on deck during both times. The town is very old, beautifully kept up and sits among amazing mountain scenery. You can spend the entire day walking around and see everything in the old city. Extremely beautiful place.