Church of England in Ireland is the Church of Ireland, so those are the records most likely to help you.
John McIntyre is a very common name. Looking at the 1901 census of Co Antrim there were 33. It’d have been equally common a hundred years earlier. Ideally you need your John’s parent’s names from a marriage or death certificate to be sure of identifying the right man.
Researching in Ireland in the 1700s and early 1800s is very hard going due to the general lack of records. If you don’t know where they lived it’s a needle in a haystack. Ideally you need to know the person’s exact denomination and the townland or parish they lived in to have any chance of finding them, and even then there may not be any records for that location.
Possibly DNA testing may be a way of matching with others who have additional information about where the family originate. Family Tree DNA reportedly has more people with Ulster roots than any other company. That obviously increases the chances of finding a match. You might want to try them or, if you have already tested, you can transfer your results to them for no fee.
The North of Ireland Family History Society is running an Ulster DNA project in conjunction with FTDNA and can offer testing kits at a reduced price. http://www.nifhs.org (Go to DNA project on the website).