Here's a picture of dinoflagellates (I seriously doubt what you have is diatoms):
As per my original post, and in agreement with Ron Shimek, physically remove the dinoflagellates, increase nutrient removal (better protein skimmer), and enusure that your source water is not problematic. In addition, along the same lines that Marc was apparently thinking; ensure your alkalinity is closer to the higher end of the scale (along the lines of 4 meq/L or so).
Assuming your water source is "clean," then syphon out the dinoflagellates and you're going to need to do a small water change every time you do so to account for the water you removed from the system.