Agnes is the English version of the Polish Agnieszka, so be sure to search for your gm's name as it was *before* she left Poland. Passenger manifests were created at the port of departure and sailed with the ship, so the names would be as they appeared on the passengers' travel papers or passports that were presented to the shipping clerk when they checked in prior to sailing. Standardized spellings of surnames didn't become necessary until about the 1930s, when receiving government benefits such as Social Security and welfare made it necessary to legally prove one's identity. Prior to that, the clerk or priest who recorded an event (birth, marriage, death, etc.) usually just spelled one's surname however it sounded to them.
Also, there are other ports through which your gm could have entered the US: Boston, Philadelphia, Baltimore, Galveston, or even a Canadian port. Have you tried searching for her in these records as well? How do you know what year Agnes immigrated?
The baptismal record you have should give her birthplace or at the very least what village the parish was located in. If she was married in the USA and you don't yet have a photocopy or transcript of the entry in the church books (not just a certificate), I'd suggest you get one. Church records tend to have more accurate spellings than civil records and tend to be a bit more precise for where the bride/groom were born. Another source for her surname would be her children's baptismal records.
-MJ