We always try to compare/contrast the fees
for ship vs. privately arranged transfers and
consider additional factors such as comfort
[pvt van vs bus] and time control [e.g. for embarkation]. Usually,but not always, the ship's tend to be a bit more expensive and sometimes, drop you only in a central spot in the destination city [if you're not going to the airport] .....but,then, they also are 'definite'. Last summer we had the experience of Elena of Rome NOT appearing.
If you are in someplace like Civitavecchia
or the port for San Jose this can be daunting, whereas if you are at the airport, taxis are
available, so it is only disconcerting.