In terms of proximity to transportation, downtown Newark is second to none in New Jersey.

With JC and Harrison, you of course have to rely on the PATH train, which can be overcrowded. Also getting to midtown on the PATH is annoying. The 33rd street PATH station is unpleasant if there's any kind of wait as its just a platform. And on weekends, the PATH from 33rd through Hoboken is a fine example of the unique combination of f-ckery that is US public transportation. The last 1/5th of a mile of track into Hoboken, the train creeps along at 5 mph while screeching at 150 db. And the whole time, you're thinking, I don't even have to go to Hoboken, and how in the hell does the Port Authority manage to lose $200M per year on a system built 100+ years ago when they can't even maintain a normal schedule on weekends?

By contrast, in Newark of course, you have more options with NJ Transit, which, sure, is more expensive but is also a lot more comfortable.

Urby is a good option if you don't mind having a wall for a kitchen and a closet for a bedroom.

For a lower cost but still solid option, check out Teachers Village.