Should I state my chronic illness as one of the reason I have few Extra curricular activities in my application for Masters Program?
For US universities, extra-curricular activities are considered important for undergraduate admissions.  But this is not the case for graduate admissions - decisions are made primarily based on your academic record, letters of recommendation, research accomplishments if any, and to a lesser extent, GRE scores.  Extra-curricular activities are not a factor, unless they are academically related (e.g. engineering clubs and competitions, outside  projects, etc).  So there's no need to mention those you have done, nor to make excuses for those you haven't.