If you're gliding with flap, then presumably, you only extended flap because you were in an overshoot situation and therefore don't require best gliding performance. But if the glide turns into an undershoot, then a more important question might be, is it viable to retract some or all of the flap?
But yes, best glide speed will be lower with flap.
Another important factor is wind - if you're gliding into a headwind, best gliding angle will be achieved by flying above best glide speed - add half the headwind to best glide speed. In case of a tailwind, it may be better to fly at the speed for minimum sink, a few knots below best glide speed.