The inspector called you on the lack of the water pipe ground because he did not see it or find it. For a metal main water pipe exiting the house underground you need to have such a grounding as described above. It's okay for that wire (grounding electrode conductor) to go all the way across the basement from the panel with the first main disconnect switch to the water pipe.
Technically, a metal main water pipe exiting the house underground counts as a grounding electrode and all grounding electrodes must be bonded (connected together with appropriate sized wires as GECs). A metal gas pipe exiting the house underground does not count as a grounding electrode but the gas piping system should also be bonded to the aforementioned grounding electrode system. A wire similar in size to a GEC can be used; here it is called a bonding jumper.
A GEC to a ground rod need not be larger than #6 copper regardless of the amperage of the electrical system.