When I did my Rochester to Boston (via the Erie Canal to Troy) tour this Sept Amtrak still had no bike carrying on some of the routes they had offered that before. I would have had to route through NYC, which I wasn't about to do. I ended up renting a car and drove home at a cost of about $120.
What time of the year are you think of? Know that some of the canal trail is along closed off remnants of the canal that are now mosquito breading "hotels". I began to count the amount of time after I would stop before the bugs became too much to tolerate. The worst spots were about 30 seconds
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If you haven't seen this route planning aid you should check it out. Andy
Erie Canal Bike Trail (bikeeriecanal.com)