Boats go to both just make sure you go to correct boat park to where you parked your car. We went this week from Liberty Park NJ and Ellis island was first, then Statue. We skipped island and captain said it doesn't go back.
Just make sure allow plenty of time for both. The boats stop going to Ellis mid afternoon so when we went, heaps of people missed out on Ellis.
I did the tour a few months ago and the ship did the first stop at Liberty Island. After you visited the Statue it was up to you if you wanted to do a second stop at Ellis Island or not. So I'm pretty sure you will visit Ellis Island after you visited the crown.
What are the prices
Ellis Island is included. Make sure you get on the correct boat after you're done with the Statue of Liberty.
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