Biological weapons use infectious and virulent microbes (Anthrax, small-pox, bacteria or viruses).
Chemical weapons use highly toxic chemical agents, typically affecting the nervous system (Sarin nerve gas, cyanide gas, etc.).
The ways these agents can be spread or disseminated are rather difficult to control. When released, they are vulnerable to a number of environmental conditions which can mitigate or severely limit their effect. We are far more prepared for the event of biochemical disasters than we were for planes slamming into skyscrapers.
I believe the federal government has a half-dozen regional biochemical response teams in place (including federal and military), which have worked closely with state and local public heath and emergency response systems to get them up to speed in order to deal with these threats. And, I'm sure that in the face of this hightened state of alert, they continue to beef-up and improve these systems (at all levels).