The harmonic whiny noise? Probably just your rotor rubbing on one of the pads. Maybe not a problem as much as you just need to ride it and work the brakes some. But check to be certain that pad that is rubbing the rotor isn't already pushed back to the brake body as far as it can possibly go. If it is, then your rotor on the new wheel is in a slightly different position. And you'll have to adjust the brake body to give it room.

There can be other reasons too.