You did not give us the names of your ancestors, so it is difficult to give you a definitive answer; but I have run into this a few times when the ship stopped in both ports (NY and Baltimore) and the entire ships' lists were kept by the second port.
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Dear Ms. Bodenburg,
Thank you for posting your request on History Hub!
It is possible that your ancestors may have lived in Baltimore, MD for a short period. From the description Ancestry provides of the “Baltimore, Passenger Lists, 1820-1964” collection: This database also contains a few records of immigrants who entered the United States at other ports or border crossings and were later asked, when or if they were living in Baltimore, to fill out immigrant arrival information on passenger lists. Therefore, researchers may locate individuals in this database whose port of arrivals are, for example, St. Albans, Vermont; Portal, North Dakota; Port Huron, Michigan; Tampa, Florida; and others.
We suspect that your ancestors eventually arrived in New York based on the fact that their naturalization paperwork also specifies this location. Another possible explanation is that there was a scanning mix up with some New York images accidentally ending up in the Baltimore collection on Ancestry.
We searched the National Archives Catalog and located the Passenger Lists, 1817 - 1897 of vessels arriving at the Port of New York in the Records of the U.S. Customs Service (Record Group 36) that may include the ship your ancestors traveled on to New York from Germany. For more information about these records, please contact the National Archives at New York (RE-NY) at firstname.lastname@example.org. Please include the name of the ship, the travel dates, and names of your family members.
Due to the COVID-19 pandemic and pursuant to guidance received from the Office of Management and Budget (OMB), NARA has adjusted its normal operations to balance the need of completing its mission-critical work while also adhering to the recommended social distancing for the safety of NARA staff. As a result of this re-prioritization of activities, you may experience a delay in receiving an initial acknowledgement as well as a substantive response to your reference request from RE-NY. We apologize for this inconvenience and appreciate your understanding and patience.
We suggest that you review NARA’s Resources for Genealogists, as well as the History Hub Blog titled Suggestions and Advice for Family History Researchers. Also, the FamilySearch Research wikis for Germany Emigration and Immigration may be useful.
For more information about your ancestors departures from Germany, we suggest contacting the Bundesarchiv, Postfach 450 569, 12175 Berlin, Germany.
We hope this is helpful. Best of luck with your family research!
[Some information provided by Elizabeth Burnes, Subject Matter Expert]