The boat is definitely more fun, but you've hit the nail on the head recognizing that the issue is how to get to the port. The advantage to taking the CV to Sorrento is that you're probably arriving in to the train station and they're both in the same building.
As far as the "best" way to get to the port, it depends on what you mean by best. Fastest way would definitely be a taxi. Queue up at the taxi stand outside the train station, keeping an eye on your bags. (It's a rough neighborhood.)
You should be fine to buy tickets once you get to the port. It was a few years ago, but I remember lots of ticket windows. Be sure to understand which pier you need to go to for the right boat, as there are many boats leaving from there to different places. Have them write it down for you if you don't understand.