Let's face it--it's not so much the toppings that are the problem for those on a low-carbohydrate diet. It is mostly the crust and sometimes the sauce that is the problem. You do have some options, though. If you are making your own sauce, leave out the sugar in the recipe or consider using a white sauce instead. As for the crust, first, and easiest, is to reduce the amount of crust you consume. One way to do this is to make your pizza with as thin a crust as possible. You can also just eat the top of the pizza, leaving the crust.
I have also found this recipe for a low-carb pizza dough. I'll be honest here--I've never tried it, as I simply adore the real deal. But this recipe has gotten rave reviews and seem to be just the thing for anyone looking for a good substitute for a white flour-based pizza dough.