The river to the west, between Newark and Harrison, is the Passaic
River which passes through Paterson up north, flows southwards and
empties into Newark Bay; the next river, inside Jersey City, is the
Hackensack River, also emptying into Newark Bay.

Manhattan Transfer was slightly to the east and slightly to the north
of the present Harrison station. The Pennsylvania originally switched
from steam to electric power there for the trip into Penn Station [New
York] though the North River Tunnnels that were finished around 1912;
until then the Pennsy had its New York terminal in Jersey City at
Exchange Place and used ferries to Manhattan. When the Pennsy
electrified the New York Philadelphia Washington route in the 1930s,
Manhattan Transfer was no longer needed and was demolished. It was at
that same time that the new [present] Newark Penn Station was built.

The Hudson Tubes website at
http://www.hudsoncity.net/tubes/gatewaytubepage.html
has a sightseeing tour [#9] which may be helpful for out of town
visitors to the Tubes.
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Between Newark and Juornal Square the line crosses two rivers, which of
these is the Passaic, and what is the other. There are massive bridges
crossing both of these rivers, which obviously opened at one time, but I
don't think they do now. Where was Manhattan Transfer, and whos trains
served it?