There are two parts to your question. The H-1B status of your brother has no bearing on your F1 visa application. Next, the timing of your visa application - The more opportune time to apply at the US Consulate is after you start your PhD program.
With respect to your application for student visa for Canada, please contact a Canadian immigration attorney. With respect to student visa for the US, one of the key gourds for denial is failure to show sufficient ties to your home country.
You may apply for US permanent residency now; however the process will take longer than if your wife is a US Citizen. Once your wife qualifies to apply for US Naturalization, she should consider apply for the US Citizenship.