The last time I float tubed the harbor with a big swell, the swell would push the water around in the harbor causing a current that would go one way, then reverse direction, etc. as the sets came in. It was pretty wild. This time of year the boats run very limited schedules because of the weather/generally bad fishing/recent rockfish closures, and work on the boats and stuff. If you can find a day when the 1/2 day runs, they'll most likely be targetting bass or sculpin (no rockfish...). As for bass in the harbor, there's lots of sandbass and grass bass on the pilings. Just drop a little swimbait (smaller than 4") or scampi, or grub down those pilings and you'll get a few.
-Brian