Quickfix list in vim when working with ninja and clang++

all of the output generated by ninja simply appears in the quickfix window, and cannot be used to jump

That sounds like Vim cannot parse the location information out of the errors because the appropriate 'errorformat' hasn't been set.

Search around, maybe someone has already written such. Otherwise, you need to write your own compiler plugin, and then use :compiler ninja instead of :set makeprg=ninja. See :help write-compiler-plugin.