Which is the best way to ground the top layer copper pour on a PCB?
They are called stitching vias and are used for what you want: -



To avoid EMC problems you may need to have many stitching vias but, without an idea of what your PCB does or what EMC specifications you wish to comply with, it's anyone's guess as to how dense the stitching vias need to be.

It might be as simple as doing something like this: -



I've added red boxes around what look to me like stitching vias. Here's another clearer example: -