See the FAQ -- "Can I color notes individually?"
Basically...
To change an entire StaveNote (which may have multiple note heads) call:
StaveNote.setStyle({fillStyle: "blue", strokeStyle: "blue"});
To change just one note head, call:
StaveNote.setKeyStyle(index, style)
Where index is the numerical index of that pitch/notehead within the StaveNote, and style is as above.