We had our bottom done at Shelter Bay. Had them do it but you can also do it yourself. As a place, Shelter Bay sucks.
Bocas Del Toro was building a yard and it might be finished as well and there are a couple of yards on the Rio Dulce at the bridge. There are a number of yards on the West coast although the only one I know personally of is Barillias north of Costa Rica (forgot the country it's in)