There was an1892 New York State Census, but I've never seen it for NY City.
Are you sure that the people you were looking for were not at another
address in 1890? That is what the usual answer is when you don't find the
people you are looking for-the police census seems pretty thorough (they
even got my great grandparents who are in none of the federal or state
censuses although they lived in the same house for about 30 years).
If you have a passenger list in 1889 and no directory listing until 1891,
you don't have any way of knowing where the people lived, and new immigrants
moved a lot. They didn't have any possessions other than what they could
carry, and they generally stayed in one area, but they moved often.