I prefer boxing just because I enjoyed it more, but I have done both. I think Muay Thai is much more versatile obviously. In addition to having kicks, knees, and elbows, it is very devastating in the clinch. You really don't get that with boxing since it is all illegal so they don't bother teaching you.
I would say give them both a try and see which you enjoy more.
The 2014 Hit Squad (FFL)
Eddie Alvarez - Junior Dos Santos - Patricio Freire - Jessica Eye - Pat Curran