Since you’ve not disclosed what the Church teaches that you disagree with, it’s hard to say. If you reject major dogmas of the Church or Moral teachings, then I’d suggest you revisit them and see exactly why the Church teaches them, if you still disagree than speak to the priest in your niece’s parish, let him know that you have difficulties with these teachings and see if they would bar you from being her sponsor, and if he can give you the rationale for why the Church teaches them. You are free to discuss them here, however some things may be personal and better delt with in a private rather than public forum such as a board like this.