Port of Entry

I recently found my ancestors traveled 1882 aboard the Hamburg-American line. The Hamburg-American line served its port in Hoboken, New Jersey. However, the manifest of Passenger/Crew List filed in New York, New York so everyone is considered arriving in New York. Additionally the scanned Hamburg Manifest by Ancestry.com lists the arrival point as New York. Shouldn’t this be New Jersey? I’m wondering if Ancestry.com might have the wrong port listed. So before I try to make a correction, does anyone know how the ship arrival would have happened? Did the Hamburg line disembark in Hoboken, NJ but the paperwork is filed at the Customs office in NY? Or, did the shipping line disembark people in NY for Customs and then move their ships to NJ?