Over the years, we have travelled across to Nusa Lembongan on a number of occasions. If you go with one of the bigger operators, ie Bali Hai , you have a number of activities which are part of the package you purchase. See below ~
There are number of cruise companies which offer day trips, which include loads of activities during your stay on the island. Just browse on the internet.
If you choose to go with one of the fast boats out of Sanur, you really can do as you please on the island, ie snorkelling gear can be hired on the beach (Mushroom Bay) and boat rides around the island can be arranged with local boatmen. You can also take a banana boat ride.
There's also lots of walk tracks all over the island, which is another way to spend your time.