Ok, so you have an American style one piece crank/bottom bracket! When you took the crank off, was there any obvious wear or pitting on the bearing surfaces, or even the bearings themselves? This would obviously indicate the need for a new bottom bracket.
If not, when you grab the top of the crank, near the pedal, and try to move it side to side (in relation to the bike), is there any play? This would indicate an incorrectly adjusted bottom bracket. Similarly if there is any resistance on the cranks when back-pedalling, the bottom bracket is adjusted too tight. If all of this is fine, and you've stripped and serviced the bottom bracket, and rebuilt with new grease, you can probably start looking else where.
How often does the noise occur? Once per revolution of the cranks would indicate either bottom bracket (which we've in theory ruled out if you've got this far and the noise persists) or pedals. So go ahead and check the pedals. Is there play in the bearings? Are they rough or dry?
If the pedals aren't the issue, move on to the rear wheel. A donk from the rear wheel will more often occur once per revolution of your wheel, rather than once per pedal stroke. Take the rear wheel off and try spinning the axle in your hand. Again, if it feels rough or dry of grease then you may need new bearings. If the axle is hard too turn by hand, or has play in it, it will either be worn or just badly adjusted. You'll most likely need a cone spanner to properly adjust the hub, so either buy/borrow one or send it off to a bike shop.
If it only happens when you're pedalling, it is more unlikely to be the front wheel, but you can check it as above. Wheel bearing noise will generally continue when you stop pedalling, so this is a good way to rule out the bottom bracket and pedal area.
Remember to also check for things you think are silly! Loose saddle, item of clothing flapping on the frame etc have all been known to create noises that we just can't trace.
It will most likely be one of the bearings on my list above, so give them a look over and see what you find!