In Search/Spotlight, can you exclude files within $HOME/Library?
Spotlight does not index file paths as a property of a file. Thus you can't search for files by path. You also can't ask it to find or exclude files by their parent folder.

You thus need to resort to a two-step process:


Run a search against the Spotlight index. You can do so at the
command line using the mdfind command Filter the results to hide
those in your Library folder. 
You could use the  grep command. Alternatively, you can paste the results from mdfind in a spreadsheet and use that to filter the list.


You can get the results you want using the HoudahSpot application. This has the option to specify more than one search location and to exclude locations. HoudahSpot also has an option to filter search results by path. Here you can apply regular expressions.

HoudahSpot can save searches as Finder "Smart Folders".  Since the feature you are after is not supported by Finder, the restriction on locations and filters will however be lost in the process.

HoudahSpot has a concept of "Templates" that you can use to much of the same effect as "Smart Folders".

Full disclosure: HoudahSpot is a commercial product of which I am the developer.