In Ep 12, Big Duo sits on the conning tower of what appears to be a destroyed Ohio Class nuclear missle sub (based on what's left of the outer hull). I could be wrong on sub ID though.
The tail cone/stabilizer assembly of a Boeing 747 is also present at JFK "mark." This one's pretty obvious due to tailcone design and APU exhaust location.
A turbofan jet engine can be seen in the snow/dust/whatever it is at JFK mark.
The camera pans through the cockpit of an airliner, assuming it's a Boeing 747 cockpit to match the tail cone, but I don't know my aircraft cockpits that well.
In Ep 17, the scene shifts to Schwarzy finding Big Duo inside a bunker complex that's obviously been hit by anti-bunker / anti-runway bombs due to the damage. No clue where a bunker of that type would be found in the NYC area, though I'm sure there's probably something buried up there somewhere. Where's the "concrete monster" in MT when you need it...
The desert to the East includes Coney Island, as demonstrated by the large wooden rollercoaster.
RE oceangoing ships on land. Ultra-severe weather can toss ships up on shore like toy boats. Also, there's a way of attacking cities near water by nuclear weapons, which involves detonating the weapon as a water burst. Pretty sure everybody's see pictures of US weapons testing involving lots of WWII era warships and low-yield nuclear weapons.
Here's one possible explanation for the sunken stuff/multiple levels. Cities at times are built upon the ruins of previous city.
One thing I've wonder is, could the sunken portion of the city be somehow based on the "Sunken Cathedral" of legend? That imagery shows up sometimes in games such as WoW (Sunken Temple), and Skyrim (sunken fort Inalta's (sp?) Deep). Usually associated with much debauchery.
More to follow, later.
Union ... Union .... Uber Alles