Not-for-profit orgs' operations generally include "program" -- the stuff they do -- and "development" -- fundraising, grant-writing, etc.
You should write a separate cover letter for each application you submit. The cover letter should show some knowledge of each company or organization's work. Its purpose is to explain how you are the very best choice for the specific position they are offering.
Job postings for not-for-profit orgs usually mention whether the opening is in development or program. Make your cover letter responsive to the posting.
So, with respect, it's a bad idea to try to craft "one size fits all" wording for a cover letter.