More audio hacking huh Reshiram_Addict?
As others said the 3ds ROMs have not been decrypted yet, I have no ETA on that happening either. This pretty much leaves line out ripping as your main option.
If as you say there is background music at the time of the cries you want to rip you have basically two options.
Noise cancellation.
Some electrical madness that I am not sure you can even do (you could do it on older systems, not sure what the 3ds has for audio here unless you want to get really crazy).
Noise cancellation then, I hope the timer is more accurate than the one on the DS. The idea behind sounds are if you play the inverted sound (inversion filters are available in audio editors like audacity) then it will cancel out the sound in question. If your sound consists of background music plus cry then playing the inverted background music that is synced up to the initial capture will strip the background sounds.
Given however many hundred mons there are there and that you might not have a completed pokedex then you are in for a fun time. Doubly so for when someone gets access to the sounds proper your work will be rendered pointless.
I could see going to this effort for background audio tracks but this is just a lot of effort for just a few cries.