I know that most of my Irish ancestors arrived on the east coast before arriving in San Francisco. I have ancestors that came through New York, Boston, and Philadelphia. I think one even wound up in Baltimore for a while, but that research is being done by another family member so my memory is fuzzy on it.
For some it was a brief stop on their way to San Francisco (my great grandmother who came through Ellis Island in June 1904 to marry my great grandfather in San Francisco in July 1904) and others who lived on the east coast before winding up in San Francisco.
Also check Canada -- some of my non-Irish ancestors were in Canada before arriving in San Francisco.
Hope that helps!