What we now know as the Barnegat Branch Trail was the roughly three hour trip by train and ferry from Waretown to Manhattan. Originally started as the Tom’s River Railroad and extended to Waretown in 1872, the line became part of the Central Railroad of New Jersey (CNJ) in 1881.
Here is a link to 33 pictures showing this now defunct Jersey City Terminal.
Here is a rough map of the local route.
And here is the entire route to Jersey City.
Train station in Waretown:

More information can be found here:
The following shows the Barnegat Express leaving Jersey City from Track 16 at 5:22 PM
