I had the same issue. LBS thought it was the cranks so they tightened them and sent me on my way. I swear that the clicking got worse!

Then I ordered a new bottom bracket and replaced it...clicking remained.

I switched pedals with my husband, and sure enough, that was it. I was ready to buy new pedals when DH suggest I re-grease mine. It worked! So I put my old bottom bracket back on it (sold the new one on ebay), put the regreased pedals back, and made a mental note to try the easiest solutions FIRST next time.

Moral of the story: check the pedals, first. It might be an easy fix.