1. Don't use the rental car any more than you absolutely have to.
2. When (not if) you go to Stillwell Ave., take a minute to go outside and across the street; the station frontage has been restored, with some original BMT signage.
3. PATH from World Trade Center to Newark; lots of trackage to see, as well as container terminals and PATH shops.
4. Hoboken NJ Transit terminal (you could do that on your return from Newark by changing at Journal Square). There aren't as many trains now as there were before Midtown Direct started, but it's still pretty impressive (and it's in the open air) in the evening rush hour, and I don't know how many people from outside the area know about it.
5. Newark Penn Station in the evening rush hour is good for train-watching, especially at the west end of Tracks 3-4. Acela, Amtrak Regional, maybe a Florida train or the Crescent, NJT MUs and loco-hauled, diesel and electric, and multi-levels. In the evening rush hour, don't miss the thundering herd coming down the cattle chute from PATH on the upper-upper level to the east end of Tracks 3-4 every time a PATH train arrives overhead (you'll hear it arrive).
6. Jamaica in rush hour. In the evening a good place to watch the action is the east end of Tracks 6-7 or 7-8. You can watch passengers get off a train on 6 and walk through the train on 7 to board the one on 8. They're used to it.
7. If you're into light rail, the former Newark City Subway (what is it called now, Newark Light Rail?) is an interesting ride, one of the few dating from before World War II. The Hudson-Bergen Light Rail is interesting pretty much everywhere. The line to Tonnelle Ave. (rhymes with Donnelly) goes through the West Shore tunnel through the Palisades, and if you go outside you can see a plaque reading "New York West Shore & Buffalo" with a date of 1906 (?), which was removed by NJ Transit from the tunnel portal and is now displayed on a rock on the way from the Tonnelle Ave. station to the parking lot (are there railfans at NJ Transit or what?).
8. You probably won't have time, but the Staten Island Railway, formerly S. I. Rapid Transit, is a real curiosity, with 3rd rail, high platforms, and B&O color position wayside signals, through some suburban countryside, especially toward the south end. It's part of NYCTA and whatever fare instrument you're using includes it; the ferry to get there is free, and typical of the ferries that the railroads used to operate across the Hudson to their terminals on the New Jersey side.
