For a nice rail trail a short train ride from Manhattan:

http://www.westchestergov.com/parks/...tyTrailway.htm
http://www.westchestergov.com/parks/...tyTrailway.htm

The North and South County Trailways. Some nice scenic riding, especially up around the New Croton Reservoir.

Might be just past the peak foliage time though. Just be sure to check out Metro North's bike restrictions. They require permits and you can't do peak trains, but on the weekend that's no issue. The permit is only $5 per person and you can get it at Grand Central easily.

For an idea, take Metro North to Tarrytown, head east over to the Tarrytown Reservoir and pick up the rail trail there. Head north to the Croton Reservoir. Plenty of good riding in the area too, but the rail trail is flat and good for folks who don't ride often.