My 11 year old son has a form of Autism and we spend a substantial portion of our income on therapy, medical care, special Jewish and secular schooling, etc. Does some of this count towards the Mitzvah of Tzedekah? To what extent? Or, does it reduce the income amount by which Tzedeka is measured?

This is not a simple question. The answer really depends on your financial abilities. If you can give your Ma'aser Ksafim – your ten percent from your net income – and still be able to easily support your child's need – that is the right and best thing to do. If the expenses for your child's care are high and burden you, you can give as much as you can. It is very hard to give a clear figure since there is none. In any event you should always give something for Tzedakah. May Hashem send you happiness and wealth to overcome all your difficulties.