I photograph my fish at night, with the aquarium light on. Daylight tends to be too harsh, and it washes the fish's colours out. I usually also hold the camera at a 30 degree angle, as I have found this cuts down on the glare.
try not to use the flash as well if you are going to take a straight on shot. This will help to eliminate the reflection problem, or as stated take the photo on an angle.
