When you have a reflective surface like glass, the angle of incidence of the light equals the angle of reflection. So if the light comes from 45 degrees from the right, it will reflect back 45 to the left. If it's directly over the glass, it will reflect straight back (at the camera then).

source: http://en.wikipedia.org/wiki/File:Reflection_angles.svg

So you want your lights far enough to the sides that you cannot see that reflection (I'd use at least two lights, one on either side). In the figure above, if P is your light source, the light will reflect off the glass to Q. If the camera is in the middle (where it says "normal") it will not see the glare of the reflection (this assume a narrow beam of light- with larger lights, rather than one narrow line between P and Q there is a much wider band of light.

In order to remove the reflection of your camera, as James Youngman said, a polarising filter will reduce it. To eliminate it you want to do one (or both) of two things:

• Move the camera slightly off-axis if you can, so that it's not exactly overhead. Using the same angle of incidence/reflection, the reflection of the camera will not come straight back up into the camera. Like moving to the side of a mirror until you can't see your reflection. This can cause perspective problems however

• The other solution is do this work in a dark place. Illuminate your subject with lights that have grids, snoots, or barn doors to focus the light on the subject, so that your camera does not get light on it. If it is in the dark it will be invisible. You can use black cards or fabric to keep the light from illuminating the camera.

• You could also fashion a black board with a hole in it for your lens. Stick the lens through and take your photos. The reflection will then be of a black surface with a small, dark round hole, which may not show up, or can more easily be edited out in post processing

A good source for all of this is the book Light, Science and Magic