I was a fulltime bartender for a local Ground Round back in the mid 90's. Every shift, I opened with a fresh drawer and since if I had someone else work with me thru the shift, we split the tips up to that point (we they left). Management never touched the tips, and it was up to us to report what we had in tips for the federal form thingy (Curval?). I think they automatically assumed 15% of your sales as tips but you certainly made more than that.
One easy fix would be to lock the tip jar, much like a small box comment cards go in, etc.
You're in an interesting legal paradox. If you report it, you might do more harm to yourself (herself) than good.
Try this, she must have friends who are bartenders at other establishments, ask them what they'd do.
It sounds pretty unprofessional for that boss to borrow into their tip jar. But if this guy is the d*ck you say he is, he may know they have no recourse.