The OEM pads on Toyota disc brakes have shims that keep the pad from vibrating in the caliper. If you used aftermarket pads and did not replace the shims (or at least use some sort of gunk like Disc Brake Quiet on the back of the pads) then you will get the exact problem you are describing. I have replaced pads on my Toyotas since 1989 and have never had a problem with any pad as long as they were shimmed. Toyotas are notoriously fussy about this.