I've been to two great places. The Venus Room on 1st Ave is great, esp on Friday (loved the caption of the Quivering Cuban) - $3.00 Pints all night was cool too. The Rivera on Christopher and 7th Ave is also quite good (they have Guinness for $2.50 during Happpy Hour). Then there is Brady's on 82nd and 2nd Ave, not a Sox bar, but a great baseball bar, run by a Mets fan, who likes Sox fans and home to several ancient Giants and Dodgers fans who HATE the MFYs and will talk for hours about the game with anyone intelligent.
Haven't been to the Sox friendly bar by the stadium yet, but I will.