I was hoping this article would say something about improving the margin of error for this kind of statistical estimate, or at least provide a critique of mark-and-recapture statistics for counting squirrels (maybe they are just too... squirrely), but alas it sounds like they threw a bunch of volunteers at the problem:
> The trick is to divide and conquer. They drew a grid of 350 hectares—plots of land measuring 10,000 square meters—over Central Park. Think of them as something like Census tracts. Volunteers then fanned out and conducted two counts, one in the morning and another at night. The Squirrel Sighters, as they were called, spent 20 minutes per count searching for furry subjects, looking up in the trees and down in the bushes, and listening to the clawing and clucking sounds they make. Allen likens it to an Easter egg hunt; some volunteers found many squirrels, others saw none.