I don't have experience with the Toyota Sienna in particular, but having driven many different cars, this type of vibration isn't unusual. Especially on less expensive cars, there is less care taken to test vibration from speakers and its effect on interior panels. There is some damping material you can buy, but with that, you have to remove the interior panels and wrap it around the speakers. You might also be able to pull those panels and just try to tighten the screws holding the speakers in place, but that's not a guaranteed fix. The higher end audio option might have alleviated this problem, just because there would have been more care taken in fitting the system to the car.