Nusa Penida is quite a large island, roughly twice the size of Paris and the infrastructure is pretty basic so getting from one side of the island to the other can take time and occasionally be somewhat treacherous. This is why you may want to research where you are going to stay before booking all your nights in a hotel that may be quite far (like 1-hour drive) from your main points of interest. You may even perhaps want to change places during your stay.
Nusa Penida's main areas to stay are:
The North- West Coast: Toyapakeh area, The North Coast: Ped area, The North Coast: Sampalan area, The East Coast: Batu Nunnggal/Suana, The East Coast: Around Atuh beach, The South Coast: Around Kelingking, Crystal Bay, Inland.
The North-West Coast: Toyapakeh area
Toyapakeh is one of the main harbors so there is a high chance this is where you will arrive in Nusa Penida. The area has a host of restaurants for all budgets, shops and bars that you can get to on foot as well as an ATM and a money changer. It even has an ice cream parlour. It's an easy walk to the fast boat departure areas. Everything is centered around the main road though so apart from a few very local places on Toyapakeh beach (which is sandy and very pleasant), you won't be getting a beachfront room or place to eat.
The North Coast: Ped/ Sental area
About halfway up the North coast, 10 minutes from Toyapakeh is the pleasant village of Ped. It has a string of bars, restaurants and places to stay on the beach and quite a few more on the land side of the road. Walking distance to several shops and an ATM. Several of the bars have live music and there are budget (and posher) restaurants on the beach. The famous Ped temple is just around the corner and if you walk 10 minutes you'll find another string of tasty places to eat a bit away from the crowds (around Sental) and a bakery with fresh croissants on the way. Sental also has some quiet and well-priced hotels tucked away, many with incredible views and great value for money.
The North coast: Sampalan area
This is the second main harbour for Nusa Penida and there is also the smaller Buyuk harbour right next to it. Sampalan is the 'capital' of Nusa Penida so there is a big food market that turns into a night market with food stalls, many shops, ATMs and a few restaurants and bars. There are few places on the beach but for the most part, you'll find accommodation and food on the main road or in the small roads leading inland.
The East coast: Batu Nunnggal to Suana
The east coast stretch has many beautiful hotels and some cliff-perched restaurants/beach clubs with pools overlooking the sea. The view is quite fetching, with the last of the seaweed farmers going about their business in the shallows and the traditional jukung (small offriggers) boats lined up on the beaches. Apart from the actual village of Batu Nunggal which has a bakery and a few restaurants and shops, most places are pretty spread out and not easily accessible by foot. If you are looking for quiet, high end and amazing views this area is perfect.
The East coast: Around Atuh beach
There are a few beautiful hotels with breathtaking views that have opened around Atuh and Diamond Beach. You'll have easy access to these beautiful points of interest and can get there early before the crowds without getting up at the crack of dawn. There is not much in the way of bars and restaurants though ( though there are some small local places on Atuh beach open for lunch) and it's a bit out of the way.
The South Coast: Around Kelingking
If you want to be the first or last to be at the 'T-rex' rock formation in Kelingking, there are a few hotels to choose from right nearby. Just like for the Atuh area though, you are a bit away from restaurants and bar areas and don't expect much going on in the evening. Again if you like quiet and breathtaking views, definitely put this one on your list for a night.
Crystal bay
Crystal Bay now has a bit of a village with several places to stay and a host of restaurants to suit all budgets, you are within walking distance from all this and the famous beach and its beautiful sunsets. It is a bit of a drive to get anywhere else on the island though so if you want to explore the rest or have planned activities such as scuba diving with operators in other parts of the island, this may not be the ideal place to stay the night before.
Inland
If you'd rather have a quiet jungle abode during your stay on the island, there are many little gems lost inland away from everything. They often have breathtaking views and amazing amenities. Just make sure you do your research and read all the comments as some places have all the disadvantages of being away from it all but none of the advantages ( they may still be close to a noisy road for instance).
Wherever you choose to stay, enjoy the natural beauty, remember bugs and geckos are nigh impossible to keep out of rooms/bathrooms and Nusa Penida is still in its tourism infancy so you might not find everything you expected in your hotel. There are nonetheless some incredible places to stay in every part of the island.