Rule out the seatpost/saddle first:
-Grab seat/seatpost by the front of the saddle and push it around with lots of force to try to determine if it's coming from there. Seatpost/Saddle is probably the most likely spot.
-Bounce up and down while on the pedals but NOT on the saddle to see if if the clicking happens when you're not on the saddle.
If the noise isn't there when you forcibly move the saddle and still there when bouncing off the saddle, remove the shock and see if everything moves well.
It really could be anything. Suspension bearings, wheel bearings, loose axle, headset, bottom bracket, etc etc etc.