Naxos has one town, one port - and three different places to board a boat, which is the detail most likely to wreck an unprepared morning.
Agia Anna. The full-day island boats - both Koufonisia cruises and the Schinoussa-Iraklia sail - leave from Agia Anna's small fishing harbour, 15 minutes south of Naxos town by car, bus or a 6-7 euro taxi. The flagship checks in at 8:30, which means an early bus or a pre-booked taxi; the port square fills with cooler-toting families by 8:15 in August. Agia Anna's own beach and its row of breakfast cafes solve the pre-boat hour well.
Naxos town quay. The Delos-Mykonos boat and the sailing options that list "Naxos" as their departure board along or beside the town's harbour waterfront - walkable from anywhere inside the Kastro ring, but mind that cruise-ship mornings clog the old-market alleys between you and the pier.
Panermos bay. The two-hour Rina Cave trip leaves from somewhere none of the buses go: a palm-ringed bay on the far south coast, about 30 minutes by rental car, where the meeting point is literally "where the palm trees end". The drive is the price of the ticket's $33 fare - and the bay is one of the island's best, so most people stay for the beach.
Agios Prokopios side. The sunset sail lists its operation around Agios Prokopios; its exact meeting point arrives with your booking confirmation, so budget the 10-15 minute transfer in planning.
One quay-adjacent warning: Naxos town's port is shallow-draught - big ferries berth at the new pier, but everything tour-sized is a quay walk, so "at the port" directions are accurate to about 200 metres and the crew's confirmation message is the truth that counts.