Well I found out what the problem was. The front pads were worn down to 3/32 and the rotors were rusted.
I did not think it was the brakes because when I purchased the car from the Lexus dealership, they showed me the service report stating that the front pads were down to 4/32 and pulsating. As part of the Maryland vehicle inspection, they said they replaced the front pads and machined the rotors.
Now when I first test drove it, I noticed that the brakes felt soft and I really had to get on it. But I was also coming from a sedan so I thought maybe the 4runner being heavier just had mushier brakes. Plus they said the brakes were done according to the service report. So everything should be good.
I have driven the vehicle 1600 miles since I bought it. There is no way in hell that new pads could be worn down in that amount of time/miles.
So now I'm out $235 and needless to say, I was very upset when I found out about the brakes. I bought the car in Maryland and I'm in TN so that is the reason why i didn't take the car back to the original dealer.
I spoke with the sales person and she said she is going to speak with the manager and see what they can do. I should hear back from them tomorrow...