I have met a lot of people who think New York was the only port of entry for their ancestor. Not so! There were several ports of entry
The five major ports on the east coast were Boston, New York, Philadelphia, Baltimore and New Orleans along the Gulf. There were also smaller ports such as Galveston, Biloxi, Norfolk just to name a few. Don't forget the west coast as well as Canadian and Mexican border crossing stations.
If you can't find them in New York, now you know where to look!