I took Amtrak to NYC for a weekend. They get a pretty good grade on cost and service, but they have gotten pretty bad about being on time. Since they seem to be struggling with this problem regularly (1-2 hours late), it would really behoove them to simply adjust their schedule to reflect it. I have never tried to take a full sized bike on board, but it seems those are still restricted to trains with baggage cars, a rarity. Also, Buffalo still has no platform, requiring a very steep climb up train stairs to the car's interior.
In NY, I found the traffic and bike lanes exhilarating, traveling from Penn Station almost to Battery Park. My daughter and partner did not necessarily share my perspective, considering the pedestrians in Manhattan to be a severe impediment to travel. I plan to return to cycle the Manhattan Waterfront Greenway trail. Hopefully this will redeem the city, at least in the eyes of my daughter.
Brooklyn was a different story. The routes are convoluted and you have to plot out a complicated route to get most places. I found this annoying, but survived by writing the streets and turns on a piece of paper I stuck in the leg band of my cycling shorts. Dresses over my shorts helped me not stand out like a sore thumb. Most of the spandex crowd only appeared on the weekends or in the parks.