You should have just taken the U Train up to Rochester. The bird watching on Irondequoit Bay is great.
Incidentally, germane to this discussion is that the city of Rochester once had its own subway, which is now long gone. Some of the track, I’m told, is still used to deliver the rolls of paper to the newpaper printers downtown underground. I know that a couple of the old stations still exist (like the one near the Rundel Library). Rochester is AFAUIK, the only city to have a subway and let it go. By around 1950 noboidy was ridi ng it, and I’ve been told that the cards used to stop to let animals cross the track.
They built the subway by putting rails down in the depressions where the Erie canal used to be when it went through downtown (it had been routed south of the city, as the New York State Barge canal), and it was apparently tempting to use that handy depression in the ground and give continued life to taverns and stores that had grown up around the canal. But the city grew up around different streets after the canal was moved, and that path became increasingly irrelevant, so the subway didn’t serve the popuilation very well as time went by, and its purpose was replaced by standard bus routes.
There’s now quite a bit of info on the Rochester Subway on the Internet.
But it never did reach anywhere near Downstate, let alone New York City.
New York state is shaped vaguely like a triangle pointing west. I-87 runs almost on the eastern border, darned near touching Vermont near Lake Champlain. The area west of I-87 is about 95% of the state. And for the love of Pete, upstate starts at Albany, not Westchester. 
Trivia - I grew up in upstate NY, closer to Boston or Montreal (or Burlington! until the bridge fell down) than to NYC.
Westchester is upstate. North of that is Canada. 
New York City people - I’m sorry guys - are terrible with upstate. They don’t seem to realize when I say something is an “hour” away, I mean, an hour at 70 mph. They think it’s the hour it takes them to get across town! And then once we had someone come into our Albany office from NYC, around 2 PM, and say, “let’s check into the hotel and then go visit the other offices before dinner.”
You know, the Syracuse (2.5 hrs away), Rochester (4 hrs away), and Buffalo (5 hrs away)offices.
I think they just don’t realize how BIG the state is.
I have done this, and yes, it is about two hours. I happen to live at the end of the A train in Manhattan, and have also taken the subway to Brighton Beach (never again) and JFK airpirt (never, ever again).
I’ve commuted from Hoboken to a client in Queens. It’s actually pretty easy if you take the bus into Midtown.
I did a reverse commute to Jersey City, and I hated it. Bus to E to PATH. Took forever. But I also hate when I have to commute downtown, versus getting to work in midtown. Saves ~30 minutes each way, no matter what downtown commute I’ve tried.
What? No love for Northern New York (aka the REAL North Country)? And do NOT call us Upstate! I grew up in Northern New York (I can see Canada from my house!), but now live in Upstate New York. Before I moved to Albany, I considered anything south of Lake Placid “downstate”. As it turns out, I hear that Glens Falls is considered “North Country”. Um, no.
Downstate begins when you cross the Ausable.