New York has a delineation between navigable-by-fact and navigable-by-law.
Navigable-by-fact means one can travel on it, but the stream goes through private land where the land owners own the streambed. The right to travel (and to portage if necessary) is guaranteed even for recreational use (only within the last 10 years have the judgements considered recreational users) - good for canoers. However, the private landowners retain the rights to the fishery - bad for fishermen. That is why NYS has to buy fishing rights along the Beaverkill, E Branch, etc - they wouldn't need to buy the rights if they already owned them. In the Douglaston Case the owners had clear deed to the streambed dating to the original patents of land in 1792 from NYS. Therefore, the river is navigable-in-fact and one can float a driftboat down through the river, but cannot stop and fish without permission.
Navigable-by-law means the body of water is held in public trust and the bottom is owned by NYS. This includes all tidal waters, some major rivers (Hudson, Mohawk, St Lawrence) and bigger lakes. One can travel or fish on these since they are publically owned.
The distinction between the two can often require a lot of deed searching and legal opinion. If NYS has bought fishing rights on a river it can be assumed that they admit they don't already hold them. The West Branch would clearly be at least navigable-in-fact, but I don't know about the navigable-by-law. If it isn't navigable-by-law the proposal to prohibit fishing from a boat could create unintended consequences if the landowners banded together and stopped fishing and would result in a lengthy legal struggle since the fishermen would not give up without a fight.