I guess it depends on what you are looking for, we prefer the more personilized tours that you can get with the non cruise ship companies, I don't like being hurded around with big groups.
We did an excellent tour and they picked us up in Piraeus and brought us back there after. The company was Greece Cruise Excursions and Tours. http://greececruiseexcursions.com
we took a customized full day tour and got to see so much. It definitely the way to go!