I'd probably use a single color image (eg. your note-sprite) with alpha channel and then color the whole image with your base-color. So, something like in the following image (from wikimedia commons):
If your color was red, you would then color the note (all the black parts) with the same red. What you would need in addition, is a grayscale image with the shading of the note. Then combine the shading with the flat color by using blend-modes like Multiply and/or Screen.
Another, probably simpler approach would be to just have a grayscale image where you would multiply each color component with your selected color. So if you have a gray value of
0.5, and a red color
RGB(1.0, 0.0, 0.0), that would result in
RGB(0.5, 0.0, 0.0) for the given pixel.
Update: Here's an example image to illustrate what I mean with the blend-modes:
Of course you could just use the shadow layer if you don't need the highlights (which is basically the same as the simpler approach mentioned above).