A woman I know can into the US through Elizabeth, New Jersey in the early 1920s. There were and are other immigrantion points as well. Mobile, Alabama; Savannah, Georgia, and Charleston, SC come immediately to mind; othe cities along the coast also accepted immigrants.

It's not likely that anyone entered the US through southern ports between late 1860 and 1865 (although New Orleans was in Union hands during much of that period).