One thing to consider is where in Newark your job will be. If it is in downtown Newark, near Newark Penn Station, commuting should be no problem whatsoever. If it is in the Gateway Plaza group of office buildings, it is connected by bridges to Penn Station itself.
From the City to Newark, you have two main options, the PATH trains or NJ Transit. PATH is $1.50 each way, about a 25 minute ride from 33rd and Sixth, and requires a change of trains at Journal Square. You also can take it from the World Trade Center stop, which is a bit quicker and no changes are required.
NJT is a bit more expensive ($3.30 for a one way ticket, but I think you can get cheaper commuter tickets), but it is only 15 minutes from New York Penn Station (32nd & Seventh) and a direct shot.