For me there is a cut off time/distance from the ship. Once we get an hour away from the ship, unless there is very reliable and regular public transport I will always take a ship's excursion.

However if possible I prefer it to be a shuttle transfer and explore 'on your own' when you get there as I hate being trailed around as part of a large group.

This strategy paid off in Florence last year when the excursion got back late due to road works and long traffic jams on the way. We would have missed the boat had we been on a public bus service that day as we were over an hour late.