I got the car at 80k miles and it only started shaking after about 2 hours of driving. My scion has 100k miles on it now and the shaking has gotten worse even after I rotated the tires and got them balanced. It doesn't shake when I let off the gas or I'm just sitting at a light. As soon as I accelerate the car shakes, turning the wheel doesn't help with the shaking either. I feel it in the front wheels the most but its worse in the front passenger side floorboard.

I know its not the wheels.

Any ideas on what it might be?

 

Vibrations under acceleration only, is a typical symptom of a bad CV axle. I've had to replace one on my TC and a previous Honda due to having the same issue

 

I second that opinion, CV shafts.