I was having the exact same problem. I tried all configuration settings from jsconfig.json, tsconfig.json to settings.json and it didn't stop giving these css hints from node_modules.
After a lot of trying for days I remembered that you can reload VSCode with the extensions disabled. Sure enough that solved it. After knowing it's an extension that causes this, I just had to figure out which one. After disabling a hundred extensions one by one it suddenly disappeared.
The extension that caused it was HTML CSS Support by ecmel (ecmel.vscode-html-css
)
Disabling this extension solves the problem. There might be configuration settings for this specific extension to exclude node_modules or stop it from giving hints in unrelated file types.
It's much nicer to have actually useful intellisense because I stopped using intellisense due to the huge list of useless hints. Fun to have that luxury back.