Head down to Battery Park and you will be inundated with people offering to sell you tickets for boat trips to the Statue of Liberty. Another popular option is to take a ride on the Staten Island Ferry, which has the added bonus of being free to ride.
The best views of the Statue of Liberty are on the way to Staten Island and the best views of the Manhattan Skyline are on the way back to Manhattan. When you board the ferry on the way to Staten Island, get onto the right hand side of the ferry. On the way back the Manhattan Skyline is directly ahead for a lot of the journey but as you get closer the Ferry turns to left and then right. I found I got some good shots of the Manhattan Skyline initially from the right side of the Ferry (albeit from quite a distance) but the best views were from the left side as you make the final approach to shore.