I'm certainly not an expert on the Salmon River, but since I live in the area and have been there on more than a few times, let me give you these suggestions. If you want to fish in Pulaski, then hit up All Seasons Sports or Whitaker's. Based on what I have seen in other forums, stay away from Yankee Fly and Tackle like the plague. There are a number of fine holes in Pulaski to fish, however they are not strictly for fly fishing.
I've heard good things about the Douglaston Salmon Run from a guy I know who has a yearly membership. If you want a place that limits the number of people and you don't mind paying a little to fish, then this is a great place.
Douglaston Salmon Run, World-Class Salmon Fishing
If you go up to Altmar, then hit up Melinda's. She knows her stuff, is a great help and has fantastic prices to boot. She is located at the Lower Fly Fishing section. Altmar has 2 fly only sections, and if you come in November, both are open. The upper closes on Nov 30th. There are usually quite a few people fishing but no where near what I saw a few weeks ago when it was a "combat zone" out there. You won't ever be alone up there, but you won't be elbow to elbow either. If you want to move out of the fly fishing areas, there are a number of nice pools between Pulaski and Altmar.
Here are some resources you can use:
This is good if you want to know the flow rate of the river.
USGS Real-Time Water Data for USGS 04250200 SALMON RIVER AT PINEVILLE NY
Here are maps of the river for planning where to go:
FishSalmonRiver.com -- A FishUSA.com Regional Site -- Angler Maps
Here are the DEC Regs for Lake Ontario Tributary's and the fly fishing sections of the SR:
Great Lakes Tributaries Regulations - NYS Dept. of Environmental Conservation
If you have any more questions, let me know.