I did mine at IOM makati, amount i paid was 10k php. if you can reserve a slot within the next week for IOM, then i'd say go for IOM. Most people i know including myself didn't get any additional charges from IOM.
if available slot in IOM is still far away then i'd suggest you take your medical at st lukes. Based on the other fb groups i've joined, st. lukes accept a limited number of walk ins per day so make sure to get there really early, around 6am, though i've seen other people post that they lined up for the walk in medical as early as 5am... a caveat to taking your medical at st lukes is that they charge higher than IOM i think its 11k or 12k for the medical and based on people's experience with st. lukes it can go up if you can't show proof that you already have the required vaccines mandated by the canadian govt so be sure to bring your baby book with you or any proof you had those vaccinations (the doctor at IOM just asked me if I know my vaccination history, i told him yes, and enumerated those) i think what they were looking for was the hepatitis and measles vaccines..
hope above info helps!