http://www.nyscanals.gov/exvac/trail/campsites.html has the official NY towpath campsites. In addition to that, many of the towns along the way have free ( but limited ) camping facilities, usually at their town marinas. Middleport and Holley, for example.

Outside of the major cities like Rochester/Syracuse/etc, the path is primarily rural, so it's trivial to find someplace to stealth camp.

- Rich