NY and NJ do share some waters, but the overwhelming part of the Jersey coast is nowhere near NY, and vice versa. States have different regs for some fisheries as a result of the uniqueness of those fisheries, and the differences in those fisheries from one state to another.
For example, the southern end of NJ starts catching Fluke in April most every year. The flats and back bays of south Jersey are known for having fish months before the rest of the state starts catching them in any great numbers. As a matter of fact it is a great source of contention each year when the regs for our state are chosen, since there are far more anglers in the northern 2/3 of the state who often want regs that reflect their season, not the season for the southern end of the state.
NY has it's own fishery, as does NJ and every other state, and they are not necessarily the same. The Fluke fishery in Montauk is not even remotely similar to the fishery on the west end or raritan bay, let alone the differences in the Fluke fishery from the North shore of Long Island to the south shore.
It would be nice to have similar regs inside those shared bodies of water, but every time it has been proposed the enforcement people have complained it would be impossible to enforce, the data people complain there is no way to know what effect it would have on landings (smaller or larger sizes for one area of a state) yadda yadda yadda.
However, simply having the same regs for a fish like say Fluke up and down the coast simply does not work. That's why we switched from Coastwide to state by state in the first place, because so many states complained that the size limit and/or season chosen for the coast did not take into account the uniqueness of that particular state's fishery.
