Probably it would have to be across the river on NSA somewhere but I’m not sure where you could put it that wouldn’t create public access problems. Be a beautiful view, though.I think any big port town with a historical Navy presence would do with Philly, San Diego or Boston all being great choices for the museum. In my 'perfect' world I think Annapolis would be a great choice, especially as you could get some ships there with little issue, but I'm pretty sure there isn't much room for it. And then there is Norfolk, not the most convenient for tourists but you'd likely have plenty of room and it is a Navy town.
Newport would also be an interesting choice, I think.