The Harbor Defense Museum occupies part of Fort Hamilton, the still-active army post guarding the Narrows at the south end of Brooklyn. Its collection covers the forts, guns, uniforms, maps, and military engineering used to defend New York Harbor.
The setting is unusual, but access is more limited than at a normal city museum because the fort remains an active U.S. Army installation. Check current visitor rules before going, especially if anyone in your group is not a U.S. citizen.