Is it Islamically permissible for a second wife to stipulate in her will that her entire inheritance goes only to her children, to the exclusion of her husband, and does the ruling differ if there are family disputes that she fears might harm her children's inheritance?

Your will that your money goes to your children after your death is considered a bequest to an heir, which is forbidden by Islamic law and is not effective unless the rest of the heirs, including your husband, agree to it. If any of your inheritance passes to your husband and then to his wives and children from others, that is by Allah's decree in inheritance, and there should be no objection to it. We advise you not to concern yourself with something that has not yet happened.