The River Project is a marine science field station and estuarium (a museum showcasing the waters where river water and sea water meet) located on Pier 26 - a short walk from Battery Park. It's free and uncrowded. A good place to bring kids - 10 tanks in the front with shrimp, crabs, seahorses, an eel and other fish like striped bass in their natural water environment. The day we went they had a tank with a large turtle that someone had found in the Hudson River. There are some larger fish in the tanks in the back. Very friendly and informative helpful staff.
They also offer free 20 minute kayaking sessions on the other side of the building.
They get by with grants and donations so please contribute something when you visit.