The church should have included that in box 1 of your W-2. Ask them to cancel the 1099-MISC and issue a corrected W-2.
If they won't, then you need to report in as self-employment income on schedule C so that the correct self employment tax is calculated. Use employment code 813000.
Note that turbotax expects your W-2 to have boxes 3-6 blank. Then you check the box for religious wages on the special circumstances page. If your W-2 looks different, the church may not be paying you as clergy and Turbotax won't compute the correct tax without manual corrections.
This is a good resource. http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
