Ulrich Halder's website is a model of how to present information on musical instruments. Accurate, informative, detailed and with images of a quality that materially contribute to one's understanding of the flutes in his collection.
The Library of Congress has done a really good job with its online representation of the Dayton Miller Collection. It is the best institutional site by some measure, with high resolution images, (mostly) reliable information, and good search tools.
Hammy Hamilton's blog isn't always about flutes, but when it is it's always fascinating: well-considered, thought-provoking and with detailed photos.
There's information here which simply can't be found anywhere else, and Robert's books, on Rudall, Rose & Carte (and successors), and Readings in the History of the Flute are essential sources for anyone interested in the flute and flute playing, particularly in the nineteenth century. Robert's wooden headjoints for Boehm flutes are highly recommended.
Tony Bingham's website is a window onto a constantly-changing collection.
Chris Wilkes is one of the most skilful craftsmen and pre-eminent flutemakers alive today.