Epub 3 (which you indicate you're exporting as from InDesign) shouldn't need any DOCTYPE declarations for a fallback NCX file. The namespace should suffice:
Code:
<?xml version="1.0" encoding="UTF-8"?>
<ncx xmlns="http://www.daisy.org/z3986/2005/ncx/" version="2005-1">
If you get errors without the DOCTYPE present then something else must be wrong with your NCX.
Perhaps you should post a few of the "slew of errors" that result whenever you remove the doctype altogether.
Attached is a sample epub3 document (with fallback ncx) that passes the IDPF ePub 3 Validation with flying colors.