White wine vinegar, and time. Just soak a paper towel in it and let it sit on the stain a while, rub occasionally.
If the stains are IN the tank above the water line, you can use vinegar but don't get much into the tank. Be sure then it's white vinegar without additives. Small (a few milliliters in a 50 gallon tank) will do no harm, might drop the PH a point or so, but it will come back. It is commonly used for just that purpose (dropping PH) and is safe for fish so long as it is a small enough quantity to make little change. Vinegar in the tank is much more safe than almost any other glass cleaner.