Yes, so long as the bonus is not based on “profit” or surplus.  The Internal Revenue Service takes the position that it interferes with charitable motives to base compensation on net financial results.  In theory, the desire to generate the profit or surplus will cause the organization to cut corners on the cost of providing the goods or services and reduce the quality of goods or services provided.  Without having a personal interest in the profit, so the theory goes, decision makers will be more likely to spend what is necessary to do the job right.

The IRS has permitted bonuses based directly on gross revenues.  Many organizations give discretionary bonuses at the end of the year when they are sure that they will have the funds to do so.  The bonuses are treated, of course, as compensation to the employees and the total compensation must be reasonable to avoid excess benefits to “disqualified persons.”  But if you are a calendar year organization and have the funds available, you have a couple of days left to grant the bonuses for this year.