Is it possible that the person you are researching arrived in a different port?  I spent several years attempting to locate a manifest for a grandfather arriving in New York without success.  I knew he lived and died in Manhattan. I used all the strategies that have been suggested to you. 

Thinking out out of the box, I decided to use Steve Morse to search names in manifests in other ports.  I found him in a manifest on a ship that arrived in Philadelphia. Apparently, he got to NY by other means.  Morse also covers manifests for ships arriving in Boston, Baltimore, Charleston and Galveston as well as San Francisco.  It’s worth trying if all else appears to be a dead end.