> there are currently only two water tunnels for the entire NYC metro area

How are you counting this? If you mean Hudson River crossings between NJ and Manhattan, there are five: two road tunnel groups (Holland and Lincoln) and three rail grops (Upper/Lower Hudson and North River). When Gateway is complete (2030s), there will be four rail groups.

But if you mean the entire NYC metro area, there are significantly more: Manhattan <-> Brooklyn alone has the Hugh L. Carey for road traffic, and then six active subway tunnel groups. Manhattan <-> Queens has a similar number.