The easier commute really hinges on your final destination in Manhattan. Neither one is universally better than the other; they just serve different parts of the city exceptionally well.
For a trip to Lower Manhattan, especially the World Trade Center and the Financial District, Jersey City is significantly easier. The PATH train from Exchange Place or Grove Street can get you to the World Trade Center in less than ten minutes. It is a very short, simple trip across the river. Ferries also provide a quick and scenic option from Jersey City to downtown.
Newark, however, holds a major advantage for commuters heading to Midtown West. An NJ Transit train from Newark Penn Station provides a direct, one-seat ride into New York Penn Station in about 20-25 minutes. This makes it a surprisingly simple commute if you work near Herald Square, Hudson Yards, or Times Square. While Newark also has a PATH line to the WTC, the journey is longer than the one from Jersey City.
It really comes down to your final destination in NYC. Jersey City often has the upper hand for overall ease and frequency, primarily due to the PATH train system. Acting much like a subway extension, the PATH provides direct, 24/7 access to both the World Trade Center in Lower Manhattan and 33rd Street in Midtown from several convenient Jersey City stations. A commute from downtown Jersey City to the WTC can be incredibly short, sometimes under ten minutes.
Newark's main advantage is the speed of its NJ Transit trains from Newark Penn Station directly into New York Penn Station in Midtown. This route is typically faster than taking the PATH from Jersey City to 33rd Street. While Newark Penn Station also offers PATH service, it is the end of the line, resulting in a much longer and more crowded journey into the city. So, think of it this way: for the Financial District or West Village, Jersey City is almost always easier. For a quick, direct trip to the area around Penn Station and Times Square, Newark's NJ Transit is a very strong contender.
Jersey City generally offers an easier commute to NYC, mainly because its PATH train system feels like a part of the city's subway.
You have several stations throughout Jersey City, like Grove Street and Exchange Place, providing direct and frequent service to both Downtown Manhattan at the World Trade Center and Midtown up to 33rd Street. The ride can be incredibly short, just a few minutes from the waterfront to the WTC. Plus, ferry service adds another convenient option.
Newark's primary strength is the fast NJ Transit train from Newark Penn Station, which can get you to New York Penn Station in about 20 minutes. That speed is a major advantage for a Midtown commute. The catch is that this convenience is heavily concentrated around that one station. While the PATH also leaves from Newark Penn, it's the end of the line, so the trip is longer than any starting point in Jersey City.
Ultimately, Jersey City wins on flexibility, with more options spread across more neighborhoods. Newark provides a very fast option to Midtown, but your commute's ease depends almost entirely on your proximity to Newark Penn Station.