Getting to La Isla by boat is an unnecessarily complicated and confusing affair. Few foreigners attempt it, while the trickle who do probably feel a bit like Columbus stumbling ashore when they arrive.
Bus-boat combo tickets are sold from the Naviera Cubana Caribeña (NCC) kiosk in Havana's main Terminal de Ómnibus for Astro buses (not the Víazul terminal). The bus takes you to the seedy port of Surgidero de Batabanó, from where boats depart for Nueva Gerona. It is wise to book tickets at least a day in advance. Beware, even the reservation process can take several hours. Tickets cost MN$5 for the 90-minute bus journey and CUC$50 for the 2½-hour ferry ride. Note, it's not possible to buy a return ticket in Havana, meaning you'll have to go through the whole ticket-buying rigmarole again in Nueva Gerona (preferably as soon as you arrive). Theoretically there is supposed to be one boat a day from Batabanó at 1pm, with a second boat running on Fridays and Saturdays at 4pm. However, in practice, boats often run late or are cancelled. Check ahead.
You'll need to get to the bus terminal at least two hours before departure to confirm your ticket. Be prepared for queues.
On arrival at the port in Surgidero de Batabanó, more lines usher you through airport-style security and into a waiting room for a likely period of one to two hours before the boat departs.
Do not show up independently in Batabanó with the intention of buying a ferry ticket direct from the dock. Although technically possible, a number of travelers have come unstuck here, being told that the tickets have been sold out through the NCC kiosk in Havana. Furthermore, bedding down overnight in Batabanó holds little appeal for travelers.
The return leg is equally problematic. Procure your ticket as early as possible (preferably the day you arrive) from the ticket office across the street from Nueva Gerona's NCC ferry terminal. The ferry leaves for Surgidero de Batabanó daily at 8am (CUC$50), but you'll need to get there at least two hours beforehand to tackle the infamous queues. A second boat is supposed to leave at 1pm on Fridays and Saturdays (with a check-in time of 10:30am).
Before reserving tickets, ask if there are sufficient bus connections from Surgidero de Batabanó to Havana and, importantly, that you have a reservation.
Don't take anything as a given until you have booked your ticket. Isla boat crossings, rather like Cuban trains, tend to be late, break down or get canceled altogether.
Traveling in either direction you'll need to show your passport. You'll also want to carry plenty of your own refreshments.