well, if it's a squeak, my impulse would be something shoe related. Clipless pedals have enough float that you can still tub up on the crank arm.

However if it's a creak, then you have a whole new world of things that can be causing it. If it's a creak, it might be pedal spindles, bottom bracket crank bolts, seat rails, seat clamp, or any number of other things.