The API kit will test both ammonia (NH3) and ammonium (NH4+), so if you're getting a reading on your API kit, it could very well be indicating both NH3 and NH4+ are in your water. There is one tester I know of that tests for NH4+ exclusively and that's the Seachem Ammonia Alert.
I suppose if you really needed to know your NH3 levels you could use both testers and subtract the two readings. It's nice that API includes both types of ammonia though because ammonia converts to ammonium (by gaining an extra proton - H+) in lower pH water conditions, and vice versa. Therefore, by knowing the total concentration of ammonia in the water, you know how much water to remove in order to avoid the ammonia spikes that may occur if the pH in your tank increases unexpectedly.