They do run them on the Main and Bergen Lines regularly. I haven't been on one in over 2 years though. They had them on 1708, 1712, 1725, and 1727 before. All of the most recent times I took those trains, Comets showed up. I think they run 3 sets on weekdays and 2 on weekends, the rest are mostly Comet 5's, but did see some 2m's and 4's last week. Saw Multilevels on 1169 and 1120 just last week. Like I said, they run a few sets each day on that line, you just need to figure out what trains are using them. They do not run west of Suffern except if there is a breakdown and that's what's available to fill in.
Meadowlands shuttles frequently have them, but most of the time it has been running, they are using sets of 8 Comets. I think they're often NJCL sets that they threw a PL42AC on.