The Wife and I did a brewery/winery trip in September. There are some pretty solid breweries up there. Over on Keuka, try Keuka brewing, probably 45 minutes from Watkins Glen, but worth the drive. All of their offerings were solid. Great Choc Stout. A Habenaro ale was killer, that was probably one of the best beers I can think of for a hot summer afternoon, or with Mexican Food. Red Ale and Pale were also solid. This was honestly my favorite of the 8 or so we stopped at, and not that far from Seneca.
War horse and Wagner were good, Rooster Fish in Watkins Glen, had a great belgian and one of the best hamburgers I have ever eaten. Brewery and the pub have different names Think it is like Crooked Rooster. Naked Dove was great too, they had a harvest ale that would peel the enamel off your teeth, they are totally worth the trip. Two Goats....great beef sandwiches.