We flew Jet Blue out of EWR last Saturday morning. Only one person in front of us in line at the counter and 2 at security. Terminal A and B are very quiet compared to Terminal C.
We did get majorly delayed though on the monorail from the parking garage. They were running slow due to bad weather. And if you take a taxi, the traffic can sometimes get backed up around the terminals. I would plan to arrive 90 minutes to 2 hours prior to your flight, not really for security lines, but in case of traffic and other mishaps.