The Airtrain ride is about 10 minutes from the train station to Terminal B (assuming it's working), and security at most is usually around 20 minutes (obviously much less if you have Precheck). EWR has live security wait times on their website, so you can check ahead if you're nervous.

As far as Amtrak vs. NJT goes, there's virtually no time difference in that leg of the trip, so you're really only paying for a more comfortable seat for the 20-25 minute journey from NY-Penn.