I'm assuming you're using the "worthless" adjective only for the streetcars - I use the NYC Ferry regularly (a stop opened near my apt last year) and it's way better than the subway. I have to walk a bit further on the other side, but it's still way more comfortable.
However, it is a valuable augment to the surface system. The point is that it helps "connect the dots" (providing more options for people to get from A to B) - hence making the system more effective as a whole.
They don't compare remotely favorably to the subway along any axis except start-up cost (it's cheaper to buy a boat and build some piers than to build a subway tunnel).
Which is, well, hugely significant when you think about it.
But I guess those discussions will need to happen elsewhere.
Some people tried to make the math work for the L shutdown and even if you had a line of ferries just following each other as close as safely possible it wouldn’t be nearly enough. Subways are incredibly efficient at moving large numbers of people.