It's worth mentioning that another option is a taxi or car service to the Sorrento port, where, generally, larger ferries go to Naples. I suspect that service is more often than in smaller Positano, and where the boats themselves have to be physically smaller. I don't recommend taking the SITA public bus (to Sorrento) because it will be so crowded, especially at the end of the day.
I don't see either taxi or ferry as being a risky choice in June. But if you are in Sorrento and the ferry is cancelled, you would still have the option of taking the (hot, crowded, gritty) Circumvesuviana train to Naples. OTOH, if you want to transfer at the very end of the day, ferries and the Circumvesuviana may stop running earlier in the evening/afternoon.
Another issue is how far your room in Positano is from taxi or ferry access. I only mean that there can be hundreds of stair steps to negotiate to some parts of Positano. Likewise, where is your Naples hotel in relation to ferry port? A 25 Euro (made that up) flat-rate taxi fee in Naples might sway your car service decision a bit.