If you receive compensation from a company, non-profit or not, you must declare it as income.
If you receive a W-2, you are an employee. If you did not, you have to file as an Independent Contractor. You are responsible for your own taxes since none have been withheld. The non-profit may issue you a 1099-Misc for the amount of compensation.
You would prepare your return using the Self-Employed Edition which will let you take any expenses you had against the income as well.
