We decided on a ship excursion primarily because the wait for a tender from the ship to Santorini was more than one hour for those who were not on ship excursions. Then the wait to go up on the cable car was 2-3 hours as there were 3 large ships in town that day. Our excursion took us to Oia (where we did not have enough time, but that is the problem with a ship excursion), then to a winery -- where we saw spectacular views of the islands, then to Thira (Fira) which we toured on our own -- visiting the museum of ancient Thira -- which had artifacts from Akritori (which was closed) and Ancient Thira. We visited a church, had lunch in town, wandered in stores and took the cable car down to the dock where we caught a tender back to our ship. We were advised to wait until after 2 (when the other two ships were leaving)to take the cable car down -- there was no wait at that time. One of the passengers in our cable car walked up along side the donkeys -- which she described as "scary" but she did not wish to wait 2-3 hours for the cable car to Fira (Thira). It was quite hot.
We plan to return to Santorini in the future to spend more time than the cruise alloted, but were glad that we took the ship excursion which left the ship at 7 AM and allowed us ample free time in Fira (11 AM - 4 PM).