According to news reports. Seems like the biggest damage was to the aforementioned bait barge in Mission Bay.
http://www.nbcsandiego.com/news/local/Tsunami-Shatters-Barge-in-San-Diego-Bay-117836593.html

I went by the barge this morning and several boats were working to try to "piece things together..." The oddest part was the darn thing was now 180 degrees around from what it was before.

"Several Navy vessels were re-deployed to a site in the South Bay away from their piers."
http://www.portofsandiego.org/about-us/general-press-releases/2467-port-of-san-diego-reports-no-significant-tsunami-damage.html?utm_source=dlvr.it&utm_medium=twitter&utm_campaign=portofsandiego