Been awhile since I've been on... just caught this thread.
Both sides have a compelling argument. Since the railroad wasn't built high enough to freely accommodate boats, the bridges have to be moved within a reasonable time.
Now, I am not a "trekkie," but this is one situation where Spock's quote "the needs of the many outweigh the needs of the few" comes into play without question.
A train carrying hundreds of people to and from work, on a timed schedule, is more important than a few people on a boat, whether it's for leisure or business. However, it is unfair to make those boaters wait for a very long time.
There must be a compromise.
I like the idea where the bridges would be declared "closed" at certain times of the day, and open at other times -- and Metro-North would have to schedule its trains around those open times. Obviously, they would have to be off-peak hours, trains running in those periods should probably include a note to the effect of "trains may be delayed up to XX minutes due to moveable bridge activity."
Another possible idea, have boaters make "appointments" with the bridge operators. Boaters request their crossings in advance. The railroad knows ahead of time when boaters will be there, and they can plan accordingly. (Of course, the railroad would have approval or denial power, allowing them to fit the appointments into its own schedule, keeping train delays minimal.)
Either way, Metro-North can easily get the laws changed in its favor. All they have to do is begin observing the current law to the letter. As soon as a boat approaches, the bridge goes up immediately -- even if it's peak hours and overcrowded trains get stuck waiting. Will people get mad? Of course they will!
That's when the conductor comes on the PA and informs people of "Metro-North is fulfilling its federal obligation to stop for any and all boat traffic at every moveable bridge along the line. If you have any comments or concerns about this law, we encourage you to write to your elected local, state and federal government representatives."
They could even go one step further with adding "Complimentary pre-addressed envelopes for this purpose are available {at your station stop, from your conductor, at GCT, etc.}" That would take a bit of work to pull off, but who said anything worthwhile was easy?