The major federal tax implications are largely within your control.  If you don’t voluntarily agree that the LLC should be taxed as a regular corporation, it will be “disregarded” by the Internal Revenue Service. Many nonprofits chose this form for creation of new subsidiaries.  (See Ready Reference Page: “LLCs Become Entity of Choice for Subsidiaries”)

If your nonprofit is tax-exempt, the LLC is automatically tax-exempt also, without having to apply for recognition.  But all of the income and expenses of the LLC will be attributed directly to your parent corporation.  That’s fine if providing pest control services is within your exempt purpose.  If it isn’t, the net income of more than $1000 will be subject to unrelated business income tax and if it is “too much” of your activity could even lead to loss of your corporation’s exemption.  (See Ready Reference Page: “Nonprofits Often Worry About UBIT”)

If you choose to make the LLC taxable as a separate corporation, its income and expense will not be attributed to the parent and it will be treated as a separate taxable entity.  It can conduct any type of business it wants and all of its net income will be subject to ordinary corporate income tax. 

In either case, the LLC will be treated as a separate entity under state law for general liability purposes.  If you negligently kill people instead of critters, the liability is likely to be limited to the LLC and unlikely to be imposed on the parent organization.