In my view, the cracked rim is as plausible as a source of your sound as any other suggestion. The rear wheel is subject to torsional loads that rise and fall with pedaling force and disappear while coasting. Only one way to tell.
Can you share the details on your cracked rim? Type and age of rim, tire type and width and pressure?
I have had cracks develop around spoke holes in Spinergy rims and was surprised at how low their recommendations are for maximum tire pressure, which is very close to the minimum pressure recommendations from the tire manufacturer.