If you're PWMing an LED to adjust brightness then the frequency required will be too low for the slow switching of a BJT to matter since you could probably do as low as 30Hz-60Hz and get away with it due to the way the human eye works. Even if you used 120Hz it's not going to matter much. For your case, I don't think it matters much in your case which you use, but you'll have lower gate drive current with a logic level MOSFET than an NPN, whereas the NPN can be driven by very base-emitter voltages voltages (almost down to about 0.7V) since it is controlled by the base-emitter current rather than the voltage.