Right, armed with all the expert suggestions here was my New York 'transport' day. Never posted such a long essay before, but here goes. Get a map of the New York Subway before reading further!
Left hotel, which was on E35th, at 08.45 for a stroll to Grand Central Terminal, then line 7 out to Queensborough Plaza for the views.
Returned on line 7 to 34 St Hudson Yards. Hudson Yards is an area of huge redevelopment, think Canary Wharf 20+ years ago.
Walked the High Line from North to South. This is possibly of more interest to botanists than rail buffs but a nice walk none the less. The north end is a building site but it gets progressively better as you head south.
Line 2 from 14 St to Borough Hall. Visit the transport museum which was even better than I remembered. Although the shop at Grand Central Terminal is actually better stocked so if you want souvenirs I'd suggest go there.
Line A from Jay St Metro Tech to Broadway Jn. A complex Junction on three levels.
Line Z from Broadway Jn to Canal St, taking in an old train (don't know how old, it just seemed old) and the Williamsburg Bridge.
Line 6 from Canal Street to 59 St for the cable car across to Roosevelt Island. Only one car is working currently, so a 15 minute frequency. A poster didn't say how long the duration of these works lasted.
Late lunch in the calm and tranquility of the island, then line F to Lexington Av / 59 St followed by Line Q to 96 St. This is a new extension which involved a tunnel boring machine rather than cut and cover. However it was not particularly exciting, I guess the construction was the hard part.
Return on line Q to Times Square / 42 St. Times Square makes Piccadilly Circus seem like a small village.
Call in at the Red Caboose model shop on E45th. I see what you mean! Service wasn't spotty, more tabby, as a cat greeted me on arrival. To be diplomatic, if you are of a certain girth, this isn't the place to be. You would be better off at the Cock and Bull 'British' pub next door.
Return to hotel around 17.30 for a wash and brush up before heading out to the Staten Island ferry, so line 6 from 33 St to 14 St then line 5 from 14 St to Bowling Green. Took the ferry at sunset, nice views of the sun setting behind the Statue of Liberty, before returning to base on line R from Whitehall St South Ferry to 34 St Herald Square.
Finally in need of a pint or three, the pub round the corner was showing the New York Yankees ball game. After all that lot the Farmer Jon's oatmeal stout went down rather well.
So that is just a sample of what is possible in a day. And that is before Central Park, the Empire State Building, One World Trade Centre, 9/11 memorial etc. New York is huge and takes a few days to explore. Always good to save something for a subsequent trip.
Quieter day planned tomorrow, top of the One World Trade Centre in the morning, train to Philadelphia in the afternoon and a ticket for the Phillies v Cubs baseball in the evening.
Thanks to everyone for the suggestions, the only reason I didn't walk the Brooklyn Bridge, which is another great idea, is I'd done it on a previous visit.