I suppose it depends how you're producing your invoices, but I'm sure as long as it will run through an inkjet printer it will be fine - so PNG or even JPG with a white background etc should usually be fine.
It really doesn't matter. If you design and print your own invoices, then just do it in InDesign, copy your logo across from Illustrator, or place the PNG or JPEG version in there. No difference between PNG and JPEG other than you can have transparent bits. If your logo has a white background and you're printing onto white paper, a JPEG is just fine.