One need not leave Manhattan to enjoy the Fall.

Visit Central Park, walking across the Bow Bridge up to Belvedere Castle.

Or visit the Cloisters in Fort Tryon Park. Not only is the wooded park beautiful, but the views across the Hudson to the Palisades . . . wow! And if you take the bus, that's an hour!

I'm surprised noone mentioned Cold Spring, NY (unless I missed seeing it somewhere here)!
Metro North from Grand Central(about one hour or 1:15) takes you right into the middle of the town, and it's a 2 block walk to the waterfront with great views of the other side of the river (the area near West Point). Nice little walkable town (shops and restaurants) and you can take a short cab ride (or maybe even walk) to Boscobel, a historic house and garden. Good hiking in the area too

I'm not sure if its reachable by public transport, but Storm King, an outdoor sculpture garden, is around an hour from the city.

topping

Heavens,
The Chihuly show is travelling and I recommend you see it if you can (outdoors).
http://www.chihuly.com/schedule.html