I have to run a second ground for a 200 amp house service panel to a cold water pipe. Can I use a black leftover #6 Cu and just use green elect tape on each end? Or does the NEC say I could do that only on wires larger than #6? I am running 35 feet.

There is no requirement for it to even be green. Use the black and leave it.

The water bond for a 200A service is required to be at least #4cu though.