Michael Porter appeared in court Monday, and a judge set a $400,000 for Porter. It's not clear if he has a lawyer.
Authorities say Porter also prodded the woman's 12-year-old son in the chest and throat with a knife.
Mount Morris police Chief Keith Becker says both boys have been removed from the home.
Becker says the man used waterboarding to punish the 5-year-old after he ripped his backpack.
The chief says school officials notified police after noticing that the boy acting differently.