There are three major harbors from which you can go to Nusa Penida island. The first one is the most touristic harbor is called Sanur harbor located in Sanur area, to be exact in Jalan Matahari Terbit. Here there are so many speeds boat you can choose from to take you to Nusa Penida. Sanur harbor is relatively the nearest harbor from Sanur, Kuta, Nusa Dua, airport and surrounding areas. It is very crowded especially in the morning where many tourists are departing and in the afternoon during the arrival time. When you depart from Sanur harbor, it will take approximately between 30-40 minutes boat ride to reach Nusa Penida island.
The second harbor is called Kusamba/Tribuana harbor. It is located far in the eastern coast of Bali, to be exact in Klungkung/Kusamba area. It is approximately 40-60 minutes ride from Nusa Dua/Denpasar area to reach this harbor. Yes it is a long ride however there are some advantages when departing from this harbor. First, it only take you around 15-20 minutes to reach Nusa Penida. This is a good option if you dont like a long boat ride. Another advantage is that it is not as much crowded as Sanur harbor.
Last but not least, Padangbai harbor. This harbor is located in Padangbai area, Karangasem regency. This is the best choice if you plan to bring your own motorbike or car to the island. This is the only harbor where ferry ship is available.