You can use official sources such as hospital admissions, prescriptions for drugs fighting the disease you are tracking, sales of over-the-counter medicines.
CDC (cdc.gov/flu/weekly/, cdc.gov/outbreaknet/outbreaks.html, etc), WHO, EuroFlu Weekly Electronic Bulletin map official clinical data, Aurametrix uses these sources.
Several scientific studies have compared GFT, twitter, even facebook with official sources. Johns Hopkins study (pubmed/22230244) used data from local hospitals in addition to CDC.
My sampling studies too showed that social trends are surprisingly good, despite all the noise, but provide good estimates only for highly populated areas.
You might also want to check Sickweather's algorithm, healthmap, usgs disease maps and industry databases providing coverage of pharmaceutical companies and product sales.