These 3 islands are known as 'Sister Island' and hardly 1 hour from the Bali's pier area. If you are staying in Ubud, then it will take 45-60 minutes of journey form the city to the Pier which is towards Airport or Sanur beach.
You can book the trip online to save the money as its cheaper as compared to travel agents or hotel tour desks.
The tour cost aroound 6700 INR per person, which includes free hotel pickup/drop, Lunch, Snorkeling Gear, Speed boat transfer, Coffee/tea at the resort, Towel etc.
The boat leave the pie at 10:30AM and you will be requested to collect the Snorkeling gears as per your size. It takes around 45-50 minutes from the pier to the first snorkeling stop known as Crystal Bay, maybe because inspired by the crystal clear water :)