Metro-North Railroad (MNR)
You have to have a permit to bring your bike on a Metro-North train, unless you have a folding bicycle. Lifetime permits are available at staffed ticket counters for $5. Bicycles are allowed on trains except during rush hours (see restrictions), and there can be four bikes on each train on weekdays, and eight on weekends, as space allows. If you’re riding in a larger group, you can make arrangements with Metro-North beforehand.
A trip to try: Take MNR to Brewster and then ride the Old Putnam Trail south, where you can hop back on the train at White Plains to go home.
Long Island Railroad (LIRR)
You can use the same lifetime permit for LIRR as for Metro-North since they are both run by MTA. LIRR does not guarantee bicycle carriage if there is not space, and in general only allows 1 bike per car on the weekends, although in the summer they offer weekend bike trains that allow 2 bikes per car. See their website for more details.
A trip to try: Take LIRR to Massapequa station, where you can find the Massapequa Preserve Bike Path, which heads north through the Bethpage State Park.
NJ Transit Trains
You don’t need a permit to bring your bike on NJ Transit, and between 8 and 12 bikes are allowed per train depending on the day and the route. See full restrictions.
A trip to try: Take NJ Transit to Morristown, where you can bike to the Patriots’ Path, one of New Jersey’s longest rails-to-trails paths at 35 miles.
Amtrak
You can’t roll your bike onto any Amtrak trains in New York state, sadly. However, Amtrak does offer Trainside Bicycle Check-in service on a couple of lines that depart from Penn Station, including the Northeast Regional line. With an advanced reservation and a $20 fee, an Amtrak employee will meet you trainside and take your full-sized bicycle to the baggage car where passengers are not permitted, and will retrieve it for you when you reach your stop. Read more about this service here.
A trip to try: Take Amtrak to New Haven, CT, where you can hop on the Farmington Canal Heritage Trail north through Connecticut and then connect to another Amtrak station for your ride home.