This old one again.
Ferries have no special rights on SF bay. This has been established several times. A sailing acquaintance of mine even brought it up face to face with a ferry skipper one day and this was acknowledged.
Most folks make reference to the Port Captain's directive contained in SF Public Advisory 05-95, which basically says all the deep-water channels marked in the bay are considered narrow channels for the purpose of rule 9, which says vessels less than 20 meters, and all sailboats, will not impede the safe passage of a vessel that is constrained to stay within the channel.
See
http://www.uscg.mil/d11/vtssf/rule9.asp for a discussion of rule 9 on SF bay.
THe port captain's directive 05-95 used to be posted online but I can't find it any more. I have a PDF copy if anyone would like it, send me your email.
The port captain's directive "...identifies areas where deep draft commercial and public vessels routinely operate." The term "public" here refers to recreational boats.
So the focus is clearly on having small vessels stay clear of large vessels that are a) not very maneuverable and b) required to stay in the shipping channel. Ferries are a) very maneuverable and b) criss-cross the channels all the time.
So: rule 9, and the SF public advisory 05-95, do not extend to ferries, tugs, pilot boats, work boats, or other sundry "non-recreational" boats. In other words: commercial vessels (as such) don't have any more rights than non-commercial vessels.
Also, a quick perusal of the charts for the Pier 39 (or Pier 1, for that matter) area don't show any special restriction. The waters around Pier 39 are part of the eastbound lane, in which sailboats must not impede constrained vessels. But ferries ain't constrained.
Now, I would say it is only common courtesy to avoid interfering with a passenger vessel on a scheduled run, especially right next to its dock where it may be trying to maneuver in close quarters with obstructions, etc. But that's common sense, not regulatory.
Just my .02,
Bob Walden