What part of Metro Manila has the best schools?

Really depends Phil on your preference. It's hard to conclude which is the best. Maybe you can discuss it with your wife about the budget, the methods of teaching, the holistic of the school, facilities, co-ed or exclusive. :)

I wouldn't know about "best" but I usually think of it as best for my child + our lifestyle + our beliefs + our location! Here's a guide that might help: http://ph.theasianparent.com/metro-manila-preschool-guide-sy-2015-2016/