All of the colors used by Nimbus are stored as a set of
UIManager properties. You can change any or all
of these properties before you set the look and feel.  For example:
UIManager.put("nimbusBase", new Color(...));
UIManager.put("nimbusBlueGrey", new Color(...));
UIManager.put("control", new Color(...));
for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels() {
    if ("Nimbus".equals(info.getName())) {
        UIManager.setLookAndFeel(info.getClassName());
        break;
    }
}
These three base colors, nimbusBase, nimbusBlueGrey,
and control, will address most of your needs.
See a full list of color keys and their default values on the
Nimbus Defaults page.