I don't think 3" of sand is necessarily too much. A deep sand bed is only bad if its never disturbed and allowed to build up gases. Stingrays spend so much time blowing in the sand, it will pretty much keep any anaerobic pockets from forming in the first place.
I had 3-4" of sand (depending on where the fish piled it up) in my 125g tank with rays, and I've never once had an issue with it. Between the rays, dragon goby, geophagus, and pike cichlids, it was very well turned over.
That said, its not necessary to have that much sand in the tank, when you only need 1-2" to cover the bottom.
As for filtration, definitely go with either a powerful canister filter or a sump. They'll both provide adequate filtration, but the sump provides more water volume and better biological filtration.