Business & farm

I agree with @Opus 17 in that a minister is not classified as a statutory employee.

Ministers have what is termed "dual tax status"; employee for income tax purposes, but considered self-employed for social security purposes (SECA).

I will provide some thoughts which may have already been stated by @Opus 17 :

• The determining factor as to whether or not you should receive a W-2 or a 1099 must be based on the usual common-law test of employee vs independent contractor.
• Ministers who receive a 1099 (based on facts and circumstances) can most likely still receive a housing allowance, but as noted by @Opus 17 , this MUST be determined in advance.  You would need to provide the church with the necessary documents to support your request.  The church would then provide you with a letter documenting the "church board" approved housing allowance amount.
• Regardless of what is specified as a housing allowance, at the end of the year you would need to document that the housing allowance meets the test of the lesser of: (1) the amount designated either on the W-2 or other documentation as noted above, (2) the fair rental value of the residence, or (3) actual expenses incurred.
• The third sentence is not real clear.  You state "without a 1099 to enter as self-employment income".  Regardless of whether a minister receives a W-2 or a 1099, both are considered self-employment income for SE Tax purposes.  Maybe you are referring to income as reported on Sch C?
• I believe that ministers that receive a 1099 and claim a housing allowance may be more at-risk for an audit.  No proof as I'm not sure anyone understands the IRS algorithms. 
• In general, I would recommend you consult with a tax professional (who prepares multiple 1040's for ministers) who can have a one on one with you to discuss your particular situation.  In this day and age, this individual does not even have to be in your same area.