He gets money from his ex-wife, Charlene. We learn in Finding Mary McGuffin that in addition to receiving a hefty alimony, he also places purchases of various "-inators" directly onto her personal tab with vendors. She doesn't seem to have noticed or possibly doesn't care.
Doofenshmirtz: You know, I may be an evil scientist, but it doesn't take a degree purchased from the Internet with your ex-wife's money, to know how special and important you are to me.
Vanessa: That's so sweet.
Doofenshmirtz: Well, I'd better run. I bought a used -inator today at the garage sale, and it's missing one small part.
and
Owner: Alright, alright I'll talk. Okay, there's this guy. He comes in every week for a lab coat. He has me put everything on his ex-wife's tab. See, her address is on the bill.