Urine is sterile leaving the bladder but doesn't stay that way for long; it is an ideal growth medium for bacteria. I would rinse it out.
There is nothing terribly wrong with getting clean water in your baby's ears. You will not get water in the inner ear (that is the third and deepest part of the ear) or the middle ear (where ear infections occur). The outer ear ends at the tympanic membrane, which will keep everything out of the middle ear. The infant's ear canal is not deep at this point, and it should be easy enough to rinse out. While you are washing the scalp/face/etc., just let some drops of clean warm water run from the outer ear into the canal. When the canal is full, turn your baby's head so that the water runs out. If it's been a while since this happened, repeat once. Dry well with a towel, again turning your baby's head so that the canal drains.
Male infants do urinate on themselves. You would wash his face if he urinated on it, wouldn't you? Same applies to the ear. No biggie. He won't get "swimmer's ear" if that's what you're afraid of. I'd be more concerned about bacteria growing in what little urine is left in the ear canal.