You are not really asking "How to calibrate my magnetometer?" You think you are, but you aren't.
What you are really asking is: "How do you calibrate a sensor in an environment with noise and a DC offset?"
The answer to that is actually pretty simple and the comment by andrea answers it in a large part: You introduce a calibrated, known AC signal and make sure the software or firmware involved knows its magnitude.
If you equate it to voltage, the thinking may become vastly more easy:
If you have 1V maximum DC offset and you want to calibrate to an accuracy of 10mV, you introduce an accurate signal, usually square wave, so that you have time to let the peak excitation stabilise. In this case you'd probably want at least 2.2V peak-peak, so that you also force the signal under 0V. You then make sure you know that signal is accurate to half your requirement or better, so 5mV accuracy will do. And that's of course considering all the noise contributions as well.
In your case you may have several axes you want to calibrate, but their orientation is known once you insert the board, so you need either several fixed "exciters", in the form of for example, again as andrea says Helmholz coils, or you need one that can rotate and hold in position accurate enough.
Making a set-up with a bunch of Helmholz coils fixed with their point of highest uniformity around your device shouldn't be too hard. Since they have a very uniform and if your driving electronics are well designed also a good repeatability, you should be able to suppress surrounding noise and "afflict" your PCB with a strong enough known field to cancel out anything.
Really sensor calibration is always the same problem, the only thing that changes is the way you create the signal.