As a transman myself, my opinion, OP, is that you're perfectly right that your niece is a transgender boy, not a boy. She will never be a boy, by definition.
However, I can't recommend enough that you don't discuss this with her or, really, anyone in your common family. If she's just transitioned, she's simply too invested into propping that identity up. Anything negative will be taken as an attack. You will become the bigoted old aunt she will try to cut herself off from. There's no point to that.
You don't have to fake an enthusiasm you don't feel about her transition, but you can keep on being interested in her person, her life, her achievements and so on. Unless people bring it up themselves, there should be no reason for the word "trans" to ever come up at all.
So yeah, she's wrong to think she's a non-trans boy, but it really doesn't matter. This is not about who is right or wrong; it's about you not losing your connection to your niece.