RTJ's first course, Midvale Golf Club, has both 9 and 18 as par threes. Both are steeply uphill, with 9 playing 130 and 18 playing 210.
Brook Lea, a Ross course in Rochester, has this combination, with 9 at about 175 and 18 at 140 from all but the tips (171 from all the way back).
Haven't played it, but West Shore in Harrisburg, PA has both as par threes.