I live in Utica, so I'll speak up on the ones I know about, although the link ksbrain posted does have most of the ones I know of.
If you are in Central New York I highly recommend the Brewery Ommegang. The Cooperstown Brewery is small but located so close to Ommegang it is worth it. The F.X. Matt Brewing Co. (Saranac, contract brews) does a very nice tour, they even have a replica speakeasy.
If you are in the Fingerlake region Wagner Valley has an award winning Doppelbock. Roosterfish in Watkins Glen is a decent brewpub and is close to Wagner Valley. The Fingerlakes are obviously known for their wines, so my wife and I just split time between wineries and the local breweries. Also their is Earl Estates Meadery (I have never been.) And Bellwether Hard Cider, great owners, great variety of ciders over 10 I believe.
The Syracuse brew pubs are good, Empire is better than Syracuse Suds in my mind. Middle Ages (Micro) is good with some styles hitting and some missing. But there is a bar called Blue Tusk that is outstanding.
Other NY notables, Davidson Brothers (Dacker) and Sackets Harbor (1812 Amber).
Bottled: Citrus Infused Full-Bodied Weizenbier
Bottled: American Bock
Primary: AHS Special Holiday Ale