Firstly, make sure AA is turned off for Mass Effect 3, else it will force FXAA.
Then, open nVidia Inspector, and click the little screw and wrench icon to open the profile manager. At the top where it says 'Profiles' type Mass Effect, and you'll see Mass Effect III in the drop down list.
Enter the following settings (they'll be in a drop down list so no need to type them manually);
Antialiasing Compatibility = 0x080100C5 (Mass Effect, Mass Effect II)
Antialiasing Mode = Override any application settings
Antialiasing Setting = Whatever you want. I'm using 4xMSAA.
Antialiasing Transparency Multisampling = Enabled
Also, because I don't trust the in-engine settings, I also turned on;
Anisotropic Filtering Mode = User-defined / Off
Anisotropic Filtering Setting = 16x
Texture Filtering Quality = High Quality.