I agree that it doesn't seem right. But that doesn't mean that it's legally wrong. You see, New York is an "at will" employment state. At-will employment means that without a contract, you have no contractual or other right to employment with the company. The company is entitled to fire you for any reason: a good reason, a poor reason, or no reason at all--as long as the company does not fire you for an illegal reason (race, gender, age, religion, etc...). But it extends beyond firing, to hiring, promotions, demotions, wage cuts and raises, disciplinary actions, and even scheduling. Unless you can show that this was done in violation of a contract, union agreement, or a clear violation of an unambiguous and binding clause against the employer, or that it was done because of some minority status (age, race, gender, religion, disability) that you have, then they do have this discretion.
New York does not require that vacation be provided at all, and can institute policies for the forfeiture of the vacation. This is (generally) irrespective of your ability to take it or not. Now if they have "looked the other way" and not really enforced the policy for some employees but not others (that would be called "selective enforcement" of the policy) AND you could argue that they enforced it because of your disability or taking disability leave, you might have a case against them for illegal discrimination. But not giving you your vacation while you were on disability, so long as they were not discriminating against you because of your disability or your disability leave (but rather applying a policy in a neutral manner based upon the clear language of the policy itself) then it would be legal. I certainly agree that it's not "right" and that it would be better if they would pay you the disability, but under the clear policies I'm afraid that they have no legal obligation to do so.
I know this is probably not what you wanted to hear, but it is the law. I hope that clears things up anyway. If you have any other questions, please let me know. If not, and you have not yet, please rate my answer AND press the "submit" button, if applicable. Please note that I don't get any credit for the time and effort that I spent on this answer unless and until you rate it positively (good or better). Thank you, ***** ***** luck to you!