Dear fast forward July 4th 2012:
Congratulations on your job.
The landlord is required to state the type of non-refundable fees you must pay when you sign an apartment application and an agreement is made to hold an apartment for you for you.
A "holding fee" typically as you described, would roll over into the first month rent, but that must be disclosed to you in the apartment application.
You have a valid claim to the return of the "holding fee" if the application did not clearly inform you that the courtesy "holding fee" is not refundable. You should point this out and the landlord may relent.
You could sue for the money in NY Small Claims Court, but you need to file your complaint right away, or you will miss your own date, because you will be at the new job
You may complain to the New York State Attorney General's office about the non-refundable holding fee if the landlord did not disclose this to you in writing when you made your deposit.
The answer provided to you is in the nature of general information. The general proposition being that you should try to avoid a bad outcome if you can.