I personally wouldn't touch the actual third party source ( like changing the encapsulation ) and reason is their style might mess up.
But to handle this , I give you couple of solutions : 
1-- Ugly :  
You can override whatever you want from a component ( probably your top level component ) if it's viewEncapsulation is none .
So go to your app.ts and change the encapsulation to none and the do what ever you want inside that : 
  inside your app.scss or css
    md-input {
       input { color:red} 
     // or whatever style you want to override , sometimes you'll need !important .
    }
2-- Better : 
Material has some variables.scss file that you'll fine in their source and you can easily override their variables , like colors and stuff .
In general, you can override a global css only if the component that your doing the overriding from , it's encapsulation is none , otherwise your styles wont go outside of that component.