Yes. In a QR code the dark bits are always interpreted as data so the dots always need to be a darker color than the background. The reliability of the QR code is also determined by the contrast difference between the dots and the background, so pale grey dots on a white background will be difficult for some scanning devices to read and the code may not function properly.
Short version: Choose whatever colors you want but always make sure the dots are a significantly darker colour than the background - we suggest at least 70% darker to ensure reliable scanning.
...and always test your QR code to make sure it works using the colors you've chosen.