It all depends on how long it takes for Immigration to clear the ship's arrival. If the ship had called on another Greek port directly prior to the call on Athens, then it shouldn't take too long to clear. On an average, 30 minutes is usualy the standard time. The port for Athens is actually in neighboring Pireaus and is easily visited from Athens, however traffic is horrendous.
Check out www.EuropePortReviews.com
for detailed information on how to do each port on your own with ease and on a budget.
Have a great cruise!