Starting navigation in Waze with Android's Intents
Fix you uri to:
String uri = "waze://?ll=40.761043, -73.980545&navigate=yes";
(added navigate=yes) and you should be good.
If this is still relevant you can use this:
String uri = "geo: latitude,longtitude";
startActivity(new Intent(android.content.Intent.ACTION_VIEW,
Uri.parse(uri)));
Today's Waze
base url is https://waze.com/ul
so to navigate you have to use
https://waze.com/ul?ll=45.6906304,-120.810983&navigate=yes