I think staying in or around Newark is a bad idea. You are not going to be happy or feel safe in any urban hotel in that general area. I'm not saying you won't be safe, becuase you will be if you proceed with apporpriate caution, but you won't FEEL safe.
If your goal is to come up to this area for a while & take public transportation into NYC I suggest you look at some place a bit more suburban like Morristown, New Brunswick or Princeton. All of those towns have cosmopolitan feels but aren't gigantic cities like NY & all are on train lines so you won't have to drive into NYC which can be overwhelming if you have never done it, especially on a weekday.
If you really want to stay in the Newark area, I suggest either the Hilton above Penn Station or the Robert Treat Hotel if you are going to be here during the week. Do not stay in any property located on Routes 1 & 9. The properties out by the airport which are technically in Elizabeth & are near the Jersey Gardens Mall don't have easy trasnportation to the Path or NJ Transit but they are safe, clean & cheap.
Edited: 2:17 pm, February 11, 2013