It’s good to know that the LIRR allows small dogs in carriers on board, but it’s even better to learn about a fun day trip from NYC to the beaches on Fire Island using the LIRR. Gotham Unleashed, a blog I just found about having a pet in NYC, suggests taking the LIRR to Bay Shore (on the Babylon Branch) and walking to the ferry to Fire Island (three ferries leave for Fire Island; the one you want from Bay Shore is Fire Island Ferries — leashed dogs are allowed on board, for a round-trip fee of $7.50). Check out the Gotham Unleashed post for more information.
[6/12/11 Tragically, you can’t any more — the post is gone, and so is the site. All that’s left are the few clues I mention here. I can point you to a post on AnimalTourism.com, with some helpful tips about getting to/from Fire Island with a dog (in their case, two lively Beagles).]