Gettin' Around New York Town

Found this great bit of NYC dog transport information on Urbanhound - NYC

this is an awesome city dog website, btw.

With a little effort, you can take your hound just about anywhere in the City. In most cases, however, getting around town on public transport depends on the kindness of train conductors and bus drivers; so behave!

If all else fails, call a pet taxi (for taxi listings, go to urbanhound's services directory). Note: none of the restrictions below apply to service dogs, who, by law, are allowed just about everywhere.–Parke M. Chapman

New York City Taxis and Limousines	Contact: 311 www.ci.nyc.ny.us/html/tlc/ Taxi and limo drivers aren't obliged to transport your dog—but many will. The smaller your hound, the better your chances. The key is to be polite: ask the driver if he wouldn't mind; reassure him that your dog is clean, well-mannered and quiet. Tip well. For a small fee, most limousine companies will let you bring along your dog as long as you give notice when making a reservation.
MTA Subways and Buses	Contact: 718-330-1234 www.mta.nyc.ny.us/nyct Dogs in kennels or bags are allowed on the City's subways and buses. That said, there is a restriction that states "no big dogs." Unfortunately, there's no official definition of a "big dog," which is to say that the conductor's discretion decides whether a big dog gets on or not. So be smart: travel with your hound during off-peak hours. One of our sources told us she takes her dog on the subway in a shopping cart.
Staten Island Ferry	Contact: 311 http://home2.nyc.gov/html/dot/html/ferrybus/statfery.shtml#conduct Only dogs in kennels are allowed on the ferry.
New York Waterways	Contact: 800-533-3779 www.nywaterway.com Dogs in kennels or bags are allowed on these private inter-borough ferries.
Metro-North Railroad	Contact: 212-532-4900 www.mnr.org/mnr Dogs are allowed as long as they do not, in the words of a Metro-North spokeswoman, "become offensive to your fellow commuters." Unless your dog is tiny, it's best to travel during off-peak hours. Restrain your dog, either by leash or kennel. As well, Metro-North recommends that dog owners arrive early to clear their dog with the conductor (they "appreciate that").
New Jersey Transit	Contact: in NJ, 800-772-2222; elsewhere, 973-762-5100. www.njtransit.com According to NJ Transit's customer service department, "Pets are allowed when they are carried in a well-secured container designed for transporting animals. Leashed animals are not permitted. Animals can be transported free of charge as long as they do not occupy a seat to the exclusion of a fare paying passenger."
PATH Trains	Contact: 800-234-7284 www.panynj.gov/path All dogs in bags or kennels are allowed on PATH trains.
Long Island Railroad	Contact: 1-718-217-LIRR www.mta.nyc.ny.us/lirr Same rule as MTA Subways and Buses (see above).
Amtrak	Contact: 800-872-7245 www.amtrak.com The rule is simple: no dogs, ever (with the exception of service dogs, of course).
Greyhound	Contact: 800-231-2222 www.greyhound.com Don't let the name fool you—Greyhound forbids all dogs, except service dogs.
Hampton Jitney	Contact: 800-936-0440 www.hamptonjitney.com The Jitney allows dogs in carriers small enough to fit under your seat or on your lap. There's a $10 charge for pets.
Zipcar	Contact: 866-494-7227 www.zipcar.com Zipcar has modified its original draconian "no dogs in the car" policy. Dogs in carriers or kennels are allowed.