Had a good time in New York - rode plenty of subway trains. The system takes a bit of getting used to on those lines with no platform indicators, no line diagrams on the trains and fairly incomprehensible announcements by the guards. Also, few maps on the stations themselves and wayfinding signs on both the subway and generally at street level are fairly abysmal. Newer rolling stock however has much better information provision including pointless announcements about minding the gap between the train and the platform when there is virtually none.
Heavy police presence on the stations including heavily armed officers, bizarrely there were also army troops at Penn station but apart from their revolvers, they werent armed.
It was interesting watching the Long Island Railroad getting ready for the evening rush hour at Jamaica, drivers walking the tracks with no-high vis jackets, loco hauled services with double deck carriages and a couple of engineering trains on the subway. The transit museum was certainly well worth a visit and also saw some heritage stock when passing the depot on line 1 near 215 Street. Traveling on the A train across the Jamaica Bay causeway was quite surreal.
Non-transport related but I certainly recommend a visit to the tenement museum in the lower east side which is a 150 year old building where the museum tells the story of some of its inhabitants and hence the history of ordinary immigrants to New York.
Once again thanks for the many suggestions - did quite a few of them.