What is the quarry operators' most essential desire? To move gravel to locations beyond the city without the city's interference.
What is the city's most essential desire? To have control and use of South Bay and the waterfront for aesthetic, recreational, and environmental purposes, and to get gravel trucks off city streets.
With the above in mind, I developed the scheme below. It is based on a major assumption that if wrong would immediately void it, but I figure it is worth putting it out there. The assumption is that the quarry operators move gravel by train to points south instead of transferring it to a barge on the Hudson waterfront. I have no idea if this would be safe (would the loads be allowed on the North-South rail line?), cost feasible (what are the efficiencies of moving gravel by train versus barge?), politically workable (would CSX, whom I presume controls the lines, allow the proposed use?) or operationally convenient (do the train lines go where the gravel needs to go, or is there a railyard downstream where an intermodal transfer could occur?). But here's how it would work.
A new private rail spur would be extended from the existing north-south railroad line, travel along the existing South Bay causeway, and terminate at the existing quarry facility on the west side of Route 9. Quarry operators would load gravel there and move it by railcar to points south without transferring it to barges at the Hudson waterfront. Holcim's ownership of the northern half of South Bay and the waterfront land and port (shown in green, and extending to the east of 9G, so that both sides of 9G remain natural) would be transferred to the city.
Rail-based scheme (click on image for larger view): A new private rail spur would allow gravel to be transported to points south without bringing it through crucial parts of Hudson and without using the deepwater port.
Some details would have to be worked out. The new rail line would have to cross Route 9G at grade. The configuration of the line east of 9G would have to be more complex than what I have shown so the rail cars could be loaded. Environmental regulators and the City of Hudson probably would want to limit and meter the amount of gravel moved via the new line. But these details seem solvable if the larger picture makes sense.
A final point: As I have written elsewhere, I do not wish for the greening of Hudson's waterfront to become part of a large scale eviction of industry from the city. Real industrial activity (locally owned and operated, not the conglomerate variety) needs to be accommodated and even intensified in some areas near the waterfront for the more general well-being of Hudson. It's another compromise that is necessary to give everyone most of what they most want. A topic to be expanded on another time.