When I wake up and do stretching I hear some sounds from my joints. What do you call this crunching sound from bone joints?
This answer explains and organizes some of the terms sketchily presented in previous answers, and adds a term or two.
Wikipedia's cracking-joints article says
Cracking joints is the action of moving joints to produce a sharp cracking or popping sound. This commonly occurs during deliberate knuckle-cracking. It is possible to crack many joints, such as...
Besides referring to this noise as cracking and popping, wikipedia mentions the terms clicking and snapping.
Cavitation, more precisely discharge cavitation, "in joint fluid is thought to cause the popping sound produced by bone joint cracking, for example by deliberately cracking one's knuckles." Cavitation is "formation and implosion of cavities in a liquid" – that is, bubbles form and collapse, releasing energy and possibly making noise.
Another source of bone joint noise is crepitus, "the grating, crackling or popping sounds and sensations experienced under the skin and joints". Wikipedia mentions that cavitation, respiratory diseases, and rough surfaces in contact due to fractures or arithritis are some of the causes of crepitus.
There are different words for it. Chiropractors often call it 'cracking the joints' when they adjust your back or neck. Other words used for this sound are snapping and popping. It is more or less up to you what word you want to use.
"My back often snap during Yoga", "Did you hear how my knee popped?" "You should not crack your neck." Etc. etc.
Perhaps you would call it crepitus.