MMSF, we normally arrange it ahead of time before leaving home. On several occassions we've also contacted taxi's on the spot (making sure they speak English) and negotiated a rate for several hours.

MMSF: We arranged everything on the dock in Florence, Rome, Naples and Malta and were fine. The ship is in port until aroound 2200 (except for Malta ) so if you get a reasonably early start you will be back in plenty of time. In Rome we saw everything the ship excursion offered and were back by around 1600, way before putting out to sea. No worries at all.