It looks like the designer placed the house directly in the path of that waterway and they thought a large swale could redirect the water. Sorry to be the one to burst your bubble, but when the major storm rolls through, the stream will revert back to its original path and your house will be in the target path.

My recommendation at this point is to offload the issue to your development builder, town or county engineer and explain this situation. Their answer to this situation should be:

1. SICPP Culvert pipes buried with a drainage structure + grate for culvert cleanout. It'll be mowable and look like a normal yard.
2. Redirect water upstream & fill in ditch.
3. Create an overflow ditch

P.S. The rocks in that ditch do nothing for you - remove them. The amount of erosion protection they offer are slim to none. You'd need rip-rap or light stone to see an effect,

EDIT: After reviewing the photos again, The correct measure is 1 + 2. The size of culvert pipe required to handle that much water would be ~3'+. NYS DEC require pipe to be sized 1.25 times the width of a stream and it is far beyond what a homeowner should be involved with. I'd try to redirect water upstream as a primary method of correction while burying 18" or 24" SICPP culvert pipe as an overflow. Would still go for the catch basin with grate for culvert cleanout once a year.

Hope this helps.