Hey I lived about 3 blocks from the Downtown Rochester one for years! I liked the brwepub down the road a few blocks... cant remember the name. They are not there now though. Not sure if they went out of business or just moved.
i've been to Milwaukee one time, for the National HOG rally, and had a blast. great town, great people. we hit Water Street brewery, and another one on the opposite end of water street. can't remember the name. wish i had enough time to go explore some more of the breweries around there.
Any company that brews in Rochester is off my list. Have you seen the Genessee River? Might as well be the Hudson. Just drive 2 hours east to the FX Matt Brewery and get some Saranac! Not that Utica is any better but they don't get their water from the city.