Urine is sterile leaving the baby's bladder, but doesn't stay that way for long; it is an ideal growth medium for bacteria. Personally, I would rinse it out, just as I would had it hit any other part of his body.
There is nothing 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 (aka the ear drum), which will keep everything out of the middle ear. The infant's ear canal is not deep or angled at this point, and it should be easy 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 (Cool water won't hurt him, but it's uncomfortable; in fact, using cold water ellicits an attack of vertigo; the test is called "cold water calorics"!) 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, and a middle ear infection is not possible this way.
I'd be more concerned about bacteria growing in what little urine is left in the ear canal than any harm from rinsing it out.