Pros of Hunter:
Better expert terrain
Opens for the season quicker
Main lift is newer and faster
Easier to ski the mountain in sections to seek out better conditions
Season passes reasonably priced
Cons of Hunter:
Lots of NYC gapers
More crowded
One overcrowded intermediate trail from the top
Easily windswept due to few trees to divide the trails up
Some very bad terrain bottlenecks
Pros of Windham:
More intermediate terrain
Nicer lodge
Larger of the two mountains (280 vs 250 acres)
Trails more natural to the land
Trails less crowded
Cons of Windham:
Takes longer to open terrain for the season
Season passes are more expensive
Main lift needs an upgrade
Less expert terrain
Shorter season (they close 1-2 weeks earlier than Hunter)
I've lived in New York my entire life.