A beautiful port and very easy to do a taxi tour. However, the old town is worth having a stroll around in. It was definitely worth the climb up to the old fort and castle ruins, but this does require moderate fitness.
Have cameras ready either when you approach motor or leave as it had some stunning scenery.
If you know there are going to be more than 2 ships in port (look up cruise timetables.com), definitely do the ship's tour as this saves time both in disembarking and queuing, and there will be a shortage of taxi drivers and buses.
The little towns of Oia and Fira can be a bit packed with tourists but the views are lovely.
It is not worth taking any sunset tours as the views from your cruise ship are the best.
It is very easy to catch the people mover from the port to venice main terminal. From here, you cross over the main canal and catch the vaporetto no 1 which is the scenic route of the grand canal. Venice is very busy, but if you want to do something a bit different then visit murano and burano which are easily accessed by the vaporetto (water taxi).
If you just want to meander through the narrow streets, no problem, but the walk from the people mover can take approx 1 hr especially if you get lost!
St Mark's Square is really just a place that is on people's tick list, but really there are lots of beautiful buildings and churches that are easy and free to view.