You are correct that the lower river is indeed a zoo, especially on weekends. I was up this past Friday, 9/28, and two weeks prior to that, 9/14, both time to the Douglaston Salmon Run. If you're not familiar with the Salmon River, DSR is 2.5 miles of private water just above the estuary. It costs $45/day (in addition to the NY license) to fish there. It is artificials only but most fisherman use flies. While it can be a true zoo on weekends (I won't go on a weekend), it is still somewhat less of a zoo than the rest of the river. During the week, especially Monday thru Thursday, it has far fewer anglers. You'll find more on Friday, typically folks who are doing a 3-day weekend. There are a couple of things that make the DSR a better experience, crowd wise, than other places on the SR. It is fairly closely patrolled and the assholes, snaggers, and pigs are evicted. (I've seen them throw guys out for being assholes and for snagging.) There is also no alcohol allowed. All of this tends to keep out the ribbon clerks, if you will.
That said, you won't be alone on the river but I've found that I can have an enjoyable day because with one exception (whom the DSR wardens tossed off the river), all the people I've come in contact with there are friendly and polite. Beyond that too, I will never be able to afford to go to the places where I could be alone and catch salmonids that large. Both Fridays I was up this year, I truly caught fish 'til my arms ached and had numerous fish take me down to the backing. Last Friday I caught the biggest brown I ever caught in my life, an 8-9 lb. football, along with kings mostly 25-30#+, cohos, and a steelhead that shot across the river in less than the blink of an eye. Like I said, I can't afford to go to the places to have this experience in solitary environment and for that reason, I'll tolerate the people I encounter.