OP, you mentioned not flying out of EWR for now. We have seen UA make comments about ATC and the delays there as well. I don't know how married you are to UA, but if it's that bad, and you are headed to JFK anyhow, could you choose a different airline. This does sound maddening, and I make a point now to avoid EWR for lots of reasons. LGA is my first choice, followed by JFK. But you have many variables because of work that others may not have,

FWIW, TSA complaints are followed up on, or at least some are. I filed one after two incidents in the same airport by the same people (tiny outstation) and made it clear I wanted action. A supervisor called and talked for quite some time and seemed to follow through. Correlation sure doesn't equal causation, but I gave the airport a go again (believe me when I say tiny means tiny), and have since taken 4 trips through there with zero repeats. Whether the complaint helped or not, I don't know, but I felt heard at least. It will not be the same with one of the busiest airports in the nation of course, but if I were that frustrated and my job was dependent on flying, I'd try all the options for sure. JFK has some nice DL and AA lounges...