Could it be two-year molars

This is how we found out my nephew had allergies. If it doesn't happen during the day he might be allergic to something in his room - if he has a pillow try replacing it or covering it with a good quality hypo allergenic pillow cover. If he sleeps with stuffed animals you could put them in ziploc bags and put them in the freezer for 24 hours, vacuum his room with a hepa vacuum, get rid of the rugs if he has any, etc. Good Luck.