Will be in Naples for 2 days this September. Want to see the AC by water, eat, walk around a bit in Amalfi and then head back to Naples. Here are a few questions for you. Thanks.
Which ferry company: NLG or Positano Jet
Date choices: Sunday or Monday
Advance tickets necessary?
Rough waters: not sure I want to go, but do they cancel for things like this? Refund if they do cancel due to weather?
Seeing the AC by water is the better option, so a good choice.
Regarding days, the weather will dictate all. It's great to be flexible. And yes, ferries are canceled because of rough seas and bad weather.
Expect crowds in the fall, there are no shoulder seasons in the area any more. And expect heat, so dress accordingly.
Hopefully others can answer the rest of your questions.
Have a great trip!