My daughter has had this problem. The new wife's input has in fact led to some ugly custody difficulties. Until finally someone in the legal system recently told her to shut up and butt out.
Like windygreen says, you need to evalute the "advice" to see if it is sound advice. However, there may be a point when the new wife may be overstepping her boundaries and her input could lead to custody issues and issues of parental alienation.
If this is the case, make sure the judge, your lawyer, your ex's lawyer and the guardian ad lidem assigned to your child in any custody proceedings are aware of any issues that could be construed as parental alienation (yes, step parents - such as the new wife - can become the main culprit in parental alientation).
When it comes to your children, ultimately it is you and your spouse who are responsible for raising the child and for the child's discipline. The new wife should not be telling you how to raise or how to disciplne your child, especially when the child is on YOUR TIME.