[otherguy]

Construct objects outside of your loop. (in the class)

public class TankDrive extends Thread {
  Joystick USB1 = new Joystick(1);
  RobotDrive drive = new RobotDrive(2,3,1,4);

  public void run(){
    while(true){
      drive.tankDrive(USB1.getRawAxis(2), USB1.getRawAxis(4));
    }
  }
}

Note, you shouldn't need to command the drivetrain in its own thread though...

Also, verify with your controller, but typically the y axis on the right analog stick of a joystick is on axis 5 (you are using 4 above). If you find that the right side of your drivetrain doesn't move as expected, this is likely your problem.