stocking foot is much nicer than bootfoot since wading boots generally provide better support that the boots attached to the waders, except for a select few companies that are starting to attach good boots. If you are only wearing them for one trip though you may not want to sink the cash into both waders and wading boots.

Felt kicks butt for wading in rocks. it can be a pain in the snow though, if you are going to NY in Oct you may need to look into a pair of the slip on chain cleats to use while waling to/from the stream.

I use breathables but i fish in them year round, i have fleece liners for cold weather wear. If you are only going to wear them on this trip neoprene might not be a bad choice, especially in Oct in NY.