Short answer: iPhone.
Long answer: I have an android powered device, the EVO 4G, and I love it. But I don't love it for its medical application prowess, I love it for being customizable. If you care about being able to "hack" or "root" your phone and tinker with the software, then you may enjoy Android more.
My experience is that the iPhone is far more accepted and integrated into medicine. I would say >70% of docs I know have iPhones. Epocrates has more features on the iPhone, gets upgraded more frequently, and there are also other more powerful medical apps for the iPhone, such as apps for reading CTs, anatomy, calculators, etc. Outside of Epocrates, I haven't found any medical apps that I bother keeping on my Android phone.
Also, with EMRs gaining traction, they seem to all sync with the iPhone and iPad, but I have yet to see one that supports Android. I expect that this trend will continue due to the iPhone already saturating the medical market and privacy concerns with the open nature of Android.
One last thing to mention: the battery on the iPhone is better (for when on overnight call). My phone lasts longer than an iPhone, but it's because I tinkered and rooted my phone. Certainly wasn't that way out of the box.
-bp