I qualify to apply for my citizenship in June and I am wondering if I have to apply to the council where I live or if I can apply to another council.

Councils have different amount of ceremony's and I think mines doesn't have that many per year.

You don't apply to the council. You apply (take the test and make the application) to DIAC. If you are successful, they then contact your council for your name to be added to their list. They then contact you. You can take the test anywhere but as far as I understand it you have your ceremony in your council area. Luck of the draw as to how many ceremonies your council holds a year compared to the next council along.