Sand, I prefer a larger sand but yes sand. Brings out more natural instincts to sift and be more active. As for as sand causing ammonia, when waste is trapped in gravel which is larger and allows for it to sink into the gravel it can cause anaerobic bacteria which can gas up. Therefore technically can cause fouled water. Not usually common in sand because sand packs much tighter not allowing waste to settle below sand, usually it floats on top of sand, unless of course you never clean it at all. Even then rays typically keep the sand stirred up from sifting. If you have good water movement you should never see waste settling in your setup.