A number of buddy boats did their bottoms at Balboa YC. I stayed on a mooring
there for 4 months and got to know the yard guys... They were very good when we left in Nov 2012.
Flamingo Marina has a haul out
and small yard, but is very expensive.
If you are crossing the canal, another option would be wait till you get to Colon. Shelter Bay Marina has a large haul out
facility. It is under new management and I can't comment on the quality.
Best bet is the Cruisers Net once you get into Panama