Removing Creak from Crank Arms / Bottom Bracket:

Loud creak when pedalling? Is it particularly on one side? And on the downward power-stroke? Chances are it will be this.

On older bikes, the square-taper where the pedal-arm attaches to the crank is prone to loud creaking, particularly where an alloy arm fits to a steel axle, which reverberates up the whole bike and can be difficult to diagnose. This is particularly noticeable after the pedal-arms have been removed for servicing. They are notoriously difficult to set back down perfectly again and this is what causes the arms to creak through the whole frame. If they are out of flush by even just a tiny bit, they can creak. So...

• If you are removing your pedal-arms for servicing or fitting new ones then remember to grease the square-taper on the crank before banging the arms on, this will help reduce creaking even if they are a tiny bit out.
• The creaking pedal-arms could simply need knocking on a bit more to get them flush and kill the creak, so loosen the locking-nut and give the arms a few good whacks and see if they will seat better.
• If the above tip doesn't work then the pedal-arm will have to come off and be re-fitted. Remove the arms, grease the square-taper and re-fit the arms making sure they go on securely and even.

https://bicycles.stackexchange.com/questions/124/creaking-from-cranks-spindle-how-to-fix