Well it depends on where you are heading to in NJ.
I commuted from Manhattan to Mountainside NJ and found it best to leave from Port Authority (42nd & Broadway) at Times Square riding the bus
The New Jersey Railway is another option, leaving from Penn Station. It is completely dependent on where you are heading in NJ. The good thing is, if you are commuting TO NJ in the morning, and to NYC in the evening, you will be traveling opposite the rush hour traffic for the most part (though there are PLENTY of people heading in both directions)
Check out the MTA website and NJ Transit website...it'll have the info you need based on where you are going.
My commute was about an hour each way...but I actually really enjoyed it. IT was the perfect opportunity to get all my reading done, which I probably would not have done much of at all if I were sitting at home.
