Wind wisstle or noise is only caused by 2 things.

1. Positive cabin pressure air excaping out leaks in the window seal.
2. Improperly placed weather stripping around the window.

I'd take the Toyota back to the installer and ask for reapplication of the weather stripping. Have them ride with you to hear the noise if needed.

The windshield seals via glue/seam sealant to the cars frame.
So This is why it wouldn't leak water in, but could wistle. The plastic weather stripping is for looks and UV protection of the glue used to hold the glass inplace.