My husband and I were in Key West in May and we opted for the trolley. The trolley has designated stops and you can get off and do the tourist thing and then catch another one. We bought our tickets at the dock (didn't book through the cruise line) I think you can also purchase them online. Our driver was good and gave alot of interesting facts and stories about Key West. Not sure how it compares (information wise) with the train.
I am taking my first trip to Key West in August. I have been advised to use the Bone Island Shuttle which is an air conditioned bus which you can ride all day and make as many stops as you wish for less than $7 for the day. Tickets can be purchased online for a discount.