There is a pretty decent subway line that connects Pireaus to the downtown Athens area. If you go to this link http://www.athensguide.com/metromap.html you can note the green line is in full operation (been running for years). Depending on the actual docking position of your ship the walk to the Pireaus station will be somewhere between 1/2 and 3/4 of a mile (its an easy walk through the pretty attractive port/city area. One warning about this line is that there has been a lot of problems with gypsy pickpockets working this line...so take special care of your valuables (a good idea anywhere in Europe).
Are you looking for just transport or did you want to see a lot of Athens but not with the cruise line tours?
Athens Greece Cruise Excursions and Tours is an option if you want to have someone show you around, and you can choose the places that you visit as well as lenght of time you are there. Make sure to save time to eat at the Plaka and shop a little, the food was to die for!
Here is the link to the Pireaus port guide. Bottom of the page at Travellers Guide 2006 click Inside view to get a map which will help. It shows the train and bus stops. http://www.olp.gr/main_eng.htm
