SEI gets ~$1.8B/year from DHS. I doubt that's all for CERT.
Seems like not many people from the FFRDC community read or post on HN.
https://ncsesdata.nsf.gov/datatables/ffrdcrd/2016/html/FFRDC...
Also the funding model isn't quite that straightforward. As an FFRDC they receive a certain static amount every year (in the low millions) as some kind of federal grant. Everything else is income from customer work like you'd find at any other contractor. In terms of revenue, most of the big bucks probably come from DoD and not DHS.