According to either John P. Colletta (in They Came in Ships) or Michael
Tepper (in American Passenger Arrival Records), the ship captain could
count them in either port. So you have to check Ellis Island (or Castle
Garden if it was before 1892) and the final port. I'm guessing that if
someone's final destination was Fall River, they would sail into New
Bedford or possibly Boston or Providence. So check them all.
Researching: Vila Franca, Ponta Garca, Ribeira Quente, Ribeira das Tainhas,