Is ibuprofen (Advil/aleve) okay to take during stomach flu to treat headaches and cramps or will it lead to Reye's disease like aspirin?

Okay. It is okay to take ibuprofen or Naproxen while you have the stomach flu, as it will not lead to Reyes syndrome. However, these type of medications (NSAIDs) can further irritate your stomach. I would recommend trying acetaminophen first.