Well, the Parks and Trails site/book has already been mentioned. Presuming you're intending to use the canal route for the east/west portion, I'd begin out by recommending that you start in Niagara Falls; the prevailing winds are westerly along the canal, and while headwinds are not ( generally ) too bad, you may as well have the wind work for you.

You haven't provided any details--what time of year? How are you planning on returning? Camping, motels, or a mix?