Brewerton and Ess-kay both have very good reputations. I've read lots of loopers stories about one or the other of them. A lot of people seem to end up needing a bit of service about this point of their journey. They both have good haul-out capability. It might just be a matter of who can accommodate you best based on your timing of arrival. Both are conveniently located. It's also a great area to rent a car and take a couple of side trips while "stranded" there. One of the nice things about doing the loop (or just transiting the canals) is that so many marinas and yards are very use to transients coming through who are not familiar with the area and are in need of some good quick service to get them back on their way.
It's a strange situation they have as they depend on word of mouth but not just from regular customers, from a lot of one time customers just passing through. But then loopers are writers and talkers so word does get around.
Oh and if you read a couple of reviews on AC you'll see you're not the only one to hit something submerged around the locks. One of the reviews, the owner had to be towed 14 hours and through 2 locks. They were sure glad they had tow coverage.