Taking another look at the error you've received from your build, there is a possibility that this error is being thrown because NCrunch hasn't identified the .mgcb files and copied them to the workspace. If you include all .mgcb files using the 'Additional files to include' project-level configuration setting (
http://www.ncrunch.net/documentation/reference_project-configuration_additional-files-to-include), for example, using the wildcard '**.mgcb', this will tell NCrunch about these files so that they can be copied to the workspace.
Otherwise, the best option here may well be to use a
build override to prevent NCrunch from either running the monogame build steps or from including the content reference declarations.
For example:
<ItemGroup Condition="'$(NCrunch)' != '1'">
<MonoGameContentReference Include="Content\Content.mgcb" />
</ItemGroup>
If there is an import statement importing the monogame build targets, specifying a similar condition to the above on the target import tag may also suppress the monogame build steps.