If you want to go to Nusa Penida Island from Bali, the easiest and cheapest way, if you go from the capital, Denpasar is by getting to the Sanur beach and using some traditional public boat called 'jukung'. Jukung will cost you maximum around IDR. 40.000 and it will take around 90 minutes to reach Nusa Penida.
There's another option you can take if you go from Sanur. You can also take some speed boat which is a lot more expensive than jukung (could be IDR 50.000 more expensive) but also a lot more faster (50 minutes). If you want to travel with your own car/ motorbike to Nusa Penida (please noticed its only for Nusa Penida, not Nusa Lembongan and Nusa Ceningan) you can go Padang bay (on the east part of Bali,an hour drive from Denpasar) to take a ferry boat (Kapal Ro-Ro and Kapal Re-Re).
This boat will take you crossing the Badung Strait, and the trip will take around one hour to get to the Toya Pakeh Harbor in Nusa Penida Island. Beside from Padang Bay and Sanur, you can also take some jukung from Kusamba (cost you around Rp. 25.000).
There are public boats from from Sanur, Kusamba or Padang Bai in East Bali.
From Padang Bai
You can catch the daily public ferry (large boat that includes vehicles). A passenger ticket is approx Rp 16,000 each way.
There is also a smaller public ferry speed boat service that typically carries up to 20 people. This departs from Padang Bai beach side every morning. You should be at the beach side by 6:30AM to catch the public speed boat. Buy ticket from ticket office near beach and then wait until the boat has enough passengers for the boat to depart. The ticket cost is about Rp 40,000 each way.
From Benoa Harbour
Quicksilver  Runs daily cruises from Benoa Harbour in Bali to their monstrous pontoon which floats off the north western shore of Nusa Penida. The trip includes watersport activities centred on the pontoon. Rp 570,000 per person.
Caspla Bali Boat, Sanur Beach in front of Ananda Beach Hotel, ? +62 361 7912299. Speed boat service, 3 times daily to Nusa Penida. Scheduled departure from Sanur Beach at 11AM, 2PM and 4:30PM. Departure from Buyuk, Nusa Penida at 8AM, 12:30PM and 4PM. One way fare Rp 200,000/person and return Rp 400,000/person.
Maruti Express, Sanur Beach in front of Ananda Beach Hotel, ? +62 819 1626 8871. The first speed boat service to Nusa Penida. Scheduled departure from Sanur Beach at 10AM and 4PM and departure from Nusa Penida at 9AM and 3PM. One way fare Rp 250,000/person and return Rp 480,000/person.
From Nusa Lembongan
Public boats depart daily at 6AM close to the suspension bridge between Nusa Lembongan and Nusa Ceningan and run to Toyapakeh or Buyuk Harbour in northern Nusa Penida. There are also services from the Jungut Batu area of Nusa Lembongan to Nusa Penida. All of these can be a little 'worrying' at times and are often very crowded.
Charter boats are available, departing from and arriving at the same area as the public boats. If you are staying on Nusa Lembongan, ask at your hotel. If not, go to the shoreline close to the suspension bridge or to the beach at Jungut Batu and ask around amongst the boatmen. Rates certainly vary but expect to pay around Rp 300,000.
If you want to go straight to Nusa Lembongan from Bali, here’s the options you can have :
From Sanur Beach
* Perama. A local transfers-only operator for the budget traveller. Boat departures daily at 10:30AM. The ride across is approximately 90 min and there is no same day return option. The Sanur office of Perama can be found at Warung Pojok in Jalan Hangtuah. Daily Perama buses depart from here to Ubud, Kuta, the airport, Padang Bai (for Lombok) and Amed. Rp 100,000 per person one way.
* Public Boat (slow). Departs daily from Sanur beach at 8AM and 10:30AM in front of the Ananda Hotel or near the Grand Inna Bali Beach Hotel (depending on tide). These boats can be a bit sketchy at times, and are usually very crowded. No same day return facility. The ride across is approximately 90 min.
* Daily Fast Boat Transfer, (firstname.lastname@example.org). Crossing takes 25-30 min depending on sea conditions. Departs daily from Sanur beach at 9:30AM 11.30AM 2.30PM 4.30PM. Departs daily from Lembongan at 8AM, 9AM, 1PM and 3:30PM. Rp 150.000/person (one-way) excluding hotel transfer Rp 200,000/person (one-way) including hotel transfer. edit
* Public Speed Boat, Sanur Beach, â˜Ž +62 361 743 2344. Departs daily from Sanur beach at 9AM, 12:30PM, 3:30PM and returning at 8AM, 10:30AM and 3PM daily to Jungut Batu bay. To Mushroom Bay leaves Sanur at 11.30AM, 2:30PM and 4.30PM, and leaves Lembongan at 9AM, 1PM and 3:30PM. Book in advance as seats may be limited. Hotel transfers from Sanur, Kuta, Nusa Dua, Seminyak, Legian, and jimbaran are included when bookings are for a minimum of 2 persons. Other areas have an extra charge. Crossing time is 30 min. Private charters are available and rates are subject to negotiation. Scheduled services Rp 200,000 per person one way including hotel transfers and Rp 175,000/person excluding hotel transfers.
* Rocky Fast Cruises, â˜Ž +62 361 8012324 (email@example.com), . Reliable and very fast boat from Sanur Beach to Jungut Batu. Tickets can be purchased at the office in Jl Hangtuah, Sanur, on Sanur beach where the boat departs, and in Jungut Batu on Nusa Lembongan. Crossing takes 25-35 min depending on sea conditions. Departs Sanur 10AM, noon,12noon 2 PM and 4.30 PM. Departs Nusa Lembongan 9AM, 11 AM, 1 PM and 3.30 PM. They do hotel (limited area) & airport pickup/drop offs if you send them a message regarding your personal trip details. One way fare Rp 250,000 and return Rp 450,000 including hotel pick up and drop off.
* Scoot Cruise, â˜Ž +62 361 285522, . Fast boats from Sanur Beach which take you to Jungut Batu. Hotel transfers are included. Tickets can be bought from the Scoot office next to Dunkin' Donuts in Jalan Hangtuah opposite the Sanur Paradise Plaza Hotel, or on the beach near the departure point. Crossing takes 30-40 min. Departs Sanur 9:30AM, 1:30PM and 4PM. Departs Nusa Lembongan 8:30AM, 11:30AM and 3PM. One way fare US$27 and return US$45, including hotel pick up.
* The Tanis Lembongan Express, â˜Ž +62 361 7432344 (firstname.lastname@example.org, fax: +62 361 292441), . Daily scheduled speed boat service to Jungut Batu and Mushroom Bay taking 25-30 min, departs from from Sanur Beach near the Grand Bali Beach Hotel at 11.30AM, 2.30PM, 4.30PM. Departure from Mushroom Bay on Nusa Lembongan at 9AM, 1PM and 3.30PM. Special charters can be arranged from Sanur and Padang Bay. Rp 175,000/person one-way and Rp 350,000/person return, excluding hotel transfers. Hotel pick up transfer (Sanur, Kuta, Legian, Seminyak and Jimbaran) at an extra charge of Rp 75,000/person one-way and Rp 100,000/person return (minimum 2 persons).
* Mushroom Paradise Fast Cruises, Jl Hangtuah 78, Sanur, â˜Ž +62 361 281974 (office hr: 9AM - 5PM), +62 361 8074320 (24 hr),+ 6281 916 320356. Daily fast boat transfer, Crossing takes 25-30 min depending on sea conditions. Private charters are available and rates are subject to negotiation. Departure from Sanur Beach to Mushroom Bay at 9.30am, 11.30AM, 2.30PM and 4.30PM. Departure from Mushroom Bay to Sanur at 8AM, 9AM, 1PM and 3.30PM. Tickets can be purchased at Jl Hangtuah 78, Sanur in front of Ayu Salon (Mushroom Beach Bungalow office). Price for return (round-trip) ticket includes dropoff and pickup in Nusa Lembogan. Rp 250.000/person one-way and Rp 400,000/person return, including hotel transfers. Hotel transfers from Sanur, Kuta, Nusa Dua, Seminyak, Legian, and Jimbaran are included when bookings are for a minimum of 2 persons. Other areas have an extra charge.
From Benoa Harbour
* Bounty Cruises, â˜Ž +62 361 443765. A standard transfer is available using a high speed catamaran service. The (standard transfer) service departs daily from Benoa Harbour at 9AM and from Nusa Lembongan at 3:15PM. If you have limited time for a visit to the island, an option is to take a one day cruise to the Nusa Lembongan Bounty pontoon. On a twin-hull boat under sail you will reach the island within 90 min. Drinks and snacks are available on board. The trip includes water activities on and near the pontoon; such as banana boat, water slide, kayaking, snorkelling and glass bottom boat rides. You can also take part in a Nusa Lembongan Village tour, visit a seaweed plantation and the 'Underground House'. Fastboat transfer: US$35 one-way and US$70 return. One day cruise is US$95, buffet lunch included.
* Island Explorer Cruises, â˜Ž +62 361 728 088. A standard transfer is available by fast boat or by fast catamaran. An alternative is a day cruise by a leisurely sailing yacht or by fast catamaran ("fun ship"). The fast boat (transfer only) departs from Benoa Harbour at 10:30 AM, it returns from Nusa Lembongan at 12:30PM. The yacht (day cruise) departs from Benoa Harbour at 9AM and will be back at about 5PM. Fastboat US$23 one-way and US$40 return (hotel pick up included) or by fast catamaran US$20 one-way and US$35 return (hotel pick up excluded). Price for the day cruise is US$69 by yacht or US$79 by fast catamaran, including hotel pick up, buffet lunch & water sport activities.
Source : wikitravel.org