I would presume that there is a way to include them in the VSIX file and also know where they are on disk - at least, you could use AppDomain.CurrentDomain.GetAssemblies()
for find the IronPython assembly and Assembly.Location
to find where it is, and hope the VSIX puts the Lib directory near that. (My only experience with VSIX was a while ago and I hated it, so I can't provide much advice in that department.)
Assuming you're embedding IronPython, once you have the location you can just use ScriptEngine.SetSearchPaths
to tell IronPython where the Lib directory is. If you're shelling out to ipy.exe then set the IRONPYTHONPATH environment variable before starting it.