Is motrin or aleve (naproxen) better for knee pains from running?

No real difference: Both are nsaids and both have the same mechanism of action. Motrin (ibuprofen) tends to be shorter acting and needs to be taken every 4-6 hours while Aleve (naproxen) is longer acting and needs to be taken every 12 hours. Both will work for the knee pain.

Varies by person: Motrin, Aleve or tylenol (acetaminophen) might work best depending on the individual.