Coin-Op, Harbor Town, and Waterfront all have 4 machines, High Dive has 3 (until Monday). High Dive, Harbor Town and Waterfront's are impeccable, Coin-Op's are a little more hit-or-miss cause it's much higher volume, but generally good.
Coin-Op: No Fear, Medieval Madness, TWD Pro (50 cents), WoZ
Harbor Town: GoT Pro, CFTBL, Metallica LE, Dr. Dude
Waterfront: TWD Pro, Future Spa, IJ4, 24
There is Nickel City too in Miramar, but it's not necessarily a craft beer spot (but it is close to Green Flash and Ballast Point). TSPP, LW3, Diner and WoZ. They also have IJ4 and South Park, but I don't count those.