It would depend more on two factors (1) how well they know you and more importantly (2) how well known nationally is the letter writer.
For instance, if the program director is ME, a nobody, and the ASSISTANT program director is from Peter Rosen, the later is much, much more impressive.
Caveats are they they say something actually good, the person seems like they actually know you, and the letter reader does not have a personal grudge against the letter writer.
Also important: does the letter writer know the intended reader?
If the APD knows the PD at your favorite program, this can be a very strong letter.
If your letter-writer really likes you, you can tell that person your top programs, and that person might call someone they know at one of those programs.
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