The V2/sub combo was a pod towed by the sub, which was then to be flooded to a vertical position & then fired. Given the guidance system of the V2, even in very calm waters the bobbing around of the pod would make accuracy a joke. If a V2 aimed at Times Square hit within 10 miles of the aiming point that would be a fabulous success. Unless you were ASB lucky, the impact of one 500kg conventional warhead hitting somewhere in the 5 boroughs of NYC would be unfortunate for anyone right there, but otherwise negligible. Since no gas warhead existed for the V2 & it would take a long time to develop, even a best case scenario (using a conventional warhead that hits somewhere in NYC) is minimal. BTW in 1944/45 exactly how many Uboats towing this submerged pod will make it to the east coast of the US (and back). Odds are more Germans will die attempting the attack than Americans, and more damage (in lost resources) in the lost subs and expendable pods than any damage to NYC (or DC, Philly, Boston, etc).
A fat man or little boy falling from 35,000 feet and landing in a deep lake (the scenario that causes minimal damage) will still be damaged, internal circuitry relying on vacuum tubes (valves to you Brits) severely rearranged, explosive lenses (on plutonium bomb) distorted, and the fissile materiel literally bent out of shape. even if the bomb casing does not rupture, everything inside is going to be very hot from the fissile materiel being disrupted. Good luck reverse engineering a bomb from that mess. Even if the Nazis magically got all the tech specs & manufacturing processes blueprints for either type of bomb for Christmas 1943 there is NO WAY they could have had a weapon by May 1945. The Soviets began before the war was over, had a great deal of info from spies, had the advantage of knowing that it could be done (after 7/45) etc etc and it still took them 3 years to make a device, still not a droppable bomb.