This thread hasn't been active for a bit, but as a New Yorker with a very well behaved 60lb Shepherd Mix, I just don't agree dogs have to be kept off the subway. Yes, there are potential problems with crowded trains, and I wouldn't want my dog on a crowded train, but I've had him on the #1 a number of times, and he's always behaved beautifully, and nobody complained (and happily, no transit police showed up).
That's why the Boston T, and many other dog-friendly subway systems around the world, stipulate that dogs are only permitted during offpeak hours. It works fine, everywhere it's tried. The reason dogs aren't allowed on the NYC subway is that politicians are afraid to take the heat, and there's no real incentive for them to innovate.
On a dog-related blog I do, I have just proposed a solution--MuttroCard! People who bring large dogs onto Seattle buses and streetcars pay a fare for the dog, same as if he or she was a human. Why not institute a Proof of Payment system for people to pay a separate fare for their dogs, and get a receipt to prove they did so? The machines are already available, and there can be rules regarding when dogs can board, etc. Problems with enforcement? They didn't seem to worry about that when they banned people from moving between cars. Oh yeah, that rule is totally enforceable.
(Can't do a specific article link--if you're reading this some time after I posted, do a blog search using the word MuttroCard)
The reason Guide and Assistance dogs are allowed is that interest groups for the disabled would raise holy hell if they weren't. In fact, most dogs could cope with an offpeak subway car just as well as any guide dog. And the proof of that is that they do, in cities all over Europe, and Australia, and in Boston, and Toronto. Would there be problems with poorly socialized dogs sometimes? Sure. So? Would they begin to compare to the problems caused by poorly socialized humans?
The MTA would get millions in new revenue, subway crime would drop, and the trains would be friendlier. Let New York join the rest of the civilized world, and get over this idiotic prejudice. I pay my taxes, I pay my fares, I want to be able to take my dog around the city without having to spend a fortune on cabs. MuttroCard!