You must check out the gorges around Ithaca and Watkins Glen. Absolutely incredible. Also Letchworth State Park - miles of hiking through the "Grand Canyon of the East". This website is a great rescource for hiking anywhere in New York State: cnyhiking.com
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Spraguebrook Park in Sothern Erie Co. has a nice trail that follows the contour of a ravine system. Hunters Creek Park is also another favorite near East Aurora. Iroquois Wildlife refuge can be a blast during spring bird migrations.
There are also some good trails around Ellicottville.
The Western NY Mt Bike Association (WNYMBA) is a good resource for local trail conditions. They also do pretty much all the maintenance on trails around here.