It's a bit touristy, but Liberty Science Center has got to be on this list!

Paulus Hook was the first colonized area in JC (settled in 1633) and became the principal ferry location to Manhattan for much of the 17th and 18th centuries. The Battle of Paulus Hook was a small but fierce skirmish during the Revolutionary War, and the patriot commander Henry Lee was awarded one of the only war medals that the Continental Congress ever authorized for his leadership in the battle.