Your odds of a traffic delay are highest and your odds of waiting for a train are lowest between 5 and 6ish. I concur with the advice about taking the Red Line to the Yellow Line; the views from the bridge are among the nicest in the whole system.

If your EWR flight gets cancelled and you have United Club access, the agents there may be able to put you on Amtrak instead, at which point your have to taxi/Uber/Lyft or Metro over to Union Station.