Will you be traveling around the area quite a bit?
Coronado if you are on the island
Stone Liberty station if you are near the airport
Downtown, I enjoyed San Diego beer company but that was right after they opened. Not sure what it is like now. Monkey Paw was a cool little dive. I don't care for Mission Brewery beers but the place is cool- close to the ball park
Ballast Point, Alesmith, Hess, Green Flash (and others) is a fun run to hit consecutively and are a 20 minute drive from Stone Escondido. Never knew White Labs was right there too...
Some good tap rooms around too like Hamilton's but I never visited- near the zoo