Ian,
Are you using a webmap or just creating layers from classes like ArcGISDYnamicMapServiceLayer? If yoy are not using a web map then just setting the map.setInfoWindowOnClick(false); will work.
//
You could do something like this I think :
function someFunction() {
pointerDownListener = view.on("pointer-down", function (event) {
event.stopPropagation();
// do more stuff
});
});
someFunction would fire when the tool is selected, or something of the like.
event.stopPropogation will stop the click event from firing as it normally would, and then you can hook up your own events to fire.
Here's some documentation: stopPropagation() Event Method