Why is One Nipple Darker?

Your nipples are slightly different in color most likely due to bruising which will resolve.  Sometimes the color can be different if the nipple is not healing well but given your surgery that sounds extremely unlikely.  Given enough time thigns should settle down.  Sometimes, however, if there is a lot of bruising, the color (which comes from red blood cell components) can stain the tissues as this component (hemosiderin) stays behind.

A photo would really help to better advise. But most likely things will even in time. What does your chosen surgeon have to say? 

Hello, Your nipple color may be altered due to bruising or simply the healing process. Three weeks is very early and a lot of changes will take place in the coming months. Be patient!

Denisse, I agree that time will probably even things out. It is easy to compare the two areolas because they are side by side and can be seen together. But actually you have had two separate procedures on two different areas and it is expected that each surgical site will heal in its own way- and  it is unlikely that the bruising, swelling, numbness, etc. will be identical.Give it time(3-6 months)and it should even out.