W-2 for clergy. Box 1 has $5000 . It is housing allowance (not taxed). Should this amount be reported on line 14 as $5000, housing allowance, rather than Box 1 Wages?

Yes, the housing allowance for clergy should be reported on Line 14 of the W2, not Line 1.

The housing allowance for clergy is exempt from income taxation but is subject to self-employment tax. Having the housing allowance on Line 1 means that you will be paying income tax in it. I would suggest that you take the W2 back to the issuer and have them correct it. 

You can find out more about clergy income here.