The best solution I've found was:
https://github.com/angular/angular-cli/issues/5139#issuecomment-283634059
Basically, you need to include a dummy variable on typings.d.ts, remove any "import * as $ from 'jquery" from your code, and then manually add a tag to jQuery script to your SPA html. This way, webpack won't be in your way, and you should be able to access the same global jQuery variable in all your scripts.