I love them both but I have to give the slight edge to the anime. For one, I felt the parts of the manga that the anime adapted were better done in the show. The suspense and outcome of certain events seemed to have more effective emotional impact and build up/pacing; mainly the deaths. In the manga characters die too quickly and frequently for my liking. I also prefer the anime because it was short and had a clear beginning middle and end. And while I like suspense its hard for me to figure out where the manga is heading (I fear it might go on for far longer than necessary). The anime’s wonderful animation, dub, and music also really adRAB to its overall enjoyment.
However, I do feel the manga does a few things things better. The comedy for instance is fricken hilarious. I especially love the various facial expressions and the bonus content at the end of the volumes. Furthermore, the battles are much more exciting manga wise. For the anime I can only recall two fights I really enjoyed. I even prefer the manga counterparts of many characters such as Scar, Kirablee, Winry, Bradley, Havock, and Barry mostly because they are bit more developed and involved in the book.
FMA fans who have either not seen the anime or not read the manga should definitely do themselves a favor and check out both. They are both truly exceptional.