Try telling her that if she doesn't take her capsule every day, she will be getting her medication via a daily injection (whether or not the meds are actually available in that form). If she's scared of needles, she'll happily take her pill!
Seriously, what works for me is lots and lots of water. Occasionally one of my morning vitamin caplets will stick in my throat, but it goes down if I chug enough H2O.
Also, Lady Pi Phi is right on about explaining to your daughter about all the bad things that will happen to her if she doesn't take her meds. Even with vitamins, you can say things like "your bones will be weak" and "your immune system won't be as strong, so you'll get sick more".