Stoneyard, Swiftwater, three heads (If new building is open). I haven't been there myself but I've heard nothing but good things about Genesee's tap room. There are several other smaller breweries if you have a wide open schedule. Tap and Mallet is a great beer bar which has Crowlers. Hope that helps!
Stoneyard seems to be putting out the best beers right now. Also hit Rohrbachs brewpub on Buffalo Rd for a great lunch or dinner and some of the best craft beers you will find in Rochester. Also, as chefduff2 said, Genesee Brew House is a cool spot. Not the best beers but good food and cool atmosphere. Some other honorable mentions; - Lock 32 (Pittsford on the Erie Canal) - ROC Brewing (City) - Knuckleheads (Webster) AJs Beer Warehouse in Henrietta so you can take a haul home with you!
I will third Stoneyard, it's a slight hike from Rochester itself (30 minutes) but they make killer beers, have killer guest beers on draft, and have killer food. What more do you want? Swiftwater is great too, don't miss them.
