If you take the NJT train from the airport the most stops you could possiably have is 2. To get to Penn station NYC it will take you no longer than 45 minutes (train ride should only take about 25!)
If you don't mind a longer way take take either the train or bus to Newark Penn Station and take the path train- Anywhere from 1 hr to 1.5 hrs.
Air Train at anytime of the day is perfectly safe! When I was 23 I took it from Queens to JFK @ 4am!
do you need the fasted way?