The South Brooklyn ferry route which connects Red Hook (at the foot of Pioneer Street) with other waterfront stops in Brooklyn will begin service on June 1st. Weekend service to Governors Island will begin on June 3rd. Rides will cost $2.75 and come with free transfers. There is also an App for that, it's "NYC Ferry" App.
This ferry service is an addition to the existing NY Water Taxi service currently shuttling humans to-and-from lower Manhattan.