Yes, the damage to the Erie section of the canal is severe. I'm hearing rumors that the canal between Lks. E-16 east to Waterford will not reopen this year due to the heavy damage to dam & lock structures. The Canal Corp. is planning an announcemnt later this week on the status of the Champlain section & next week regarding the Erie. My suspicions are that the Champlain will open, but not the Erie. I've seen pics of 3 locks that are totally under water & significant damage to a dam. In '06 due to severe flooding that section of the canal was closed fom June to Labor Day, & the damage was less severe.
You can take the St Lawrence route to Lake Champlain, & enter the Champlain Canal in Whitehall. But, be aware that the Hudson River is probably going to be filled with debris, & many marinas have sustained damage. Good luck.