If the supplements are medically necessary they would be covered under an Exceptional Access Program (EAP) for OHIP (if Ontario) and other programs in other provinces. You have to apply for this and the medical doctor (MD) has to fill out the paperwork and you have to go through the process.
http://www.health.gov.on.ca/en/pro/programs/drugs/eap_mn.aspx
Generally the cost to vitamin supplements are not significant but, if the child needs inflatables the costs can add up. If in Ontario it would be a children's hospital involved in this and they would have advised you of the program and even filled it out if the treatment is in support of a diagnosed medical condition.
Just because a doctor says you should take a multi-vitamin doesn't mean it is necessary nor a medical intervention needed to support the health of the child. Lots of parents do not understand what is "advice' and what is a "medical directive" given by a doctor.
Good Luck!
Tayken