Transistor with different voltage in colector and base
When you use 9V with the 330 ohm resistor, your LED has 27mA passing through. When you use 5V the current is 15mA.

What Tom says above, if you connected the LED on the emitter in series with the 330 ohm resistor, the base's 5V drops to 3.8V across the resistor (-0.6 on the B-E of the transistor and -0.6 on the LED itself) so that would drop your current for the LED to 11mA which is less than what you had when the LED was directly connected (in series with the 330 ohms resistor) to 5V.