How can I make a plated-through hole in Eagle?
No, you don't want just a oversized via.  Step back and think about the problem a bit.  You don't just want a mounting hole, but rather a genuine electrical part.  This part should show up in the schematic, be something you place on the board, have a pin connected to a net, and a pad that connection can be routed to, just like other electrical parts.  

The correct answer is therefore to use such a part.  This would have a schematic symbol with one connection.  The package would be a thru-hole pad with the hole size matching your mounting screw and the pad diameter a little larger than the screw head diameter.  If you want this to be a ground connection, connect it in the schematic to your ground net.

I have done this before and have a few such mounting hole parts in my library, including one for a #4-40 machine screw.