Clicking sound coming from pedals/pedal spindle/crank
Papuass is correct - take it back to the shop as it is under warranty and they may have offered you a free service anyway.

Here is the complete checklist for future reference... 

I believe that you have a Shimano Altus chainset - a pressed steel number with no chainring bolts to come undone.  

As for diagnosis, you are not getting the click when you are freewheeling - that is normally a simple check to do first.  

Next, try different chainring - does the click only happen in the outer ring? This can be due to the front mech touching the crank. Also check the mech clears the outer ring with the cage staying away from the teeth.   

Now try the granny ring - this will not be using the same 'chainring bolts' and will identify if the problem is there - this I do not suspect in your case due to the construction of the chainset.  

Now try and pedal out of the saddle - do you still get the click? Sometimes the seat post can creak as you pedal and you need to check that is not it.  

Stiff link? If the click on each power stroke then it is unlikely to be the stiff link going through the chainset as this will be  different each time.  

Now for checking the pedals. There should be a smidgen of grease on the pedals and inside the crank arms. With a 15mm spanner you can take them off, check the grease and put them back in again. The pedals should be in really tight, you may want to wear a tough glove whilst putting your pedals in/taking them out. This is because you can mangle your hand on the chainset quite easily doing this. Remember that the left hand pedal has a left hand thread and the right hand pedal has a right hand thread - it is important you turn the right way.  

Now for the bottom bracket. Get a socket set - 15mm and check the crank arms are on massively tight.

Check the pedals for wear/general condition and decide whether you need to tighten up the bolts holding the cages onto the bodies. There should be some play with affordable pedals - the bearings do not have to be great - but if there is too much play consider tightening them up with the socket set, or, better still, just get a new set of pedals, maybe upgrading yourself to Shimano SPD/Time ATAC.

If that has not cured it then check the bottom bracket is inserted properly. The chances are that you will need brand specific specialist tools for this, including a crank removal tool. Again you will have left hand thread on one side and right hand side on the other side. Make sure you are not doing up when you think you are trying to take off the bottom bracket.  

With modern 'cartridge' bearing bottom bracket sets (you have one of these with octalink) it is unlikely to be penetrated with dirt/grime (giving rise to noise) but older square-peg bottom brackets can have problems with ball bearing cages falling to pieces and making quite a racket. Usually these can be repacked with new balls and grease, however, you might want to put in a new b/b - this will need to be the correct outer shell length and axle length - see your existing b/b for numbers.

There is an outside chance that there may be something up with the frame, older cr/mo frames sometimes have a really basic tube for a bottom bracket that can make itself ovaloid over time. This you can only determine with the b/b fully stripped out and when you try to put it in again.

With fairly accessible tools you can get most of the bolts tight, this may cure it and save you the 'trek' to the bike shop. Given your warranty situation you can return it to the shop and let them make a decision on how much they want to strip the bike down.