When I went for YA fantasy, I queried all YA reps unless they specifically say they don't want fantasy and then I queried all fantasy reps unless they specifically say they don't want YA.
It worked out pretty well, and I am finally getting my book, High School Heroes, published somtime next summer. So, all I can say is, go for both.
As far as the word length. Yes, 50,000 is a bit short, however, there are some YA books out there of similar length. The way I see it, write the length the story is. There is always someone who is going to tell you it's too long or too short, but I find that when I don't worry about the word count I get a better story than if I am writing under those constraints.