In an incredible boon to New York City genealogists and historical researchers, the Brooklyn Public Library recently announced that it has digitized the entire run of the Brooklyn Daily Eagle, from 1841-1955. The earlier years, 1841-1902, were digitized some years ago through a grant from the Institute of Museum and Library Services (IMLS), and the later years have just now come online through a partnership with Newspapers.com. They are all available for free, at the new website, http://newsstand.bklynpubliclibrary.org/.
It's true that the entire run of the Brooklyn Daily Eagle has long been available online through the Fulton History website, but I think that the two sites serve complementary purposes. I think the quality of the images on the Brooklyn Newsstand site is better, meaning that search results are more likely to be accurate. However, the library site's "Advanced Search" option includes only the ability to add a date or date range, which is not exactly particularly advanced. If you can navigate Fulton History's search function, you'll find a lot more flexibility there. Nonetheless, I do think that the Brooklyn Newsstand search function represents an improvement over the search function at the old Brooklyn Daily Eagle Online site through the BPL, as my searches have turned up results from the early years that I was never able to find at the previous site. (Although the original eagle.brooklynpubliclibrary.org site is still up, it will be retired in May 2014.)
While Newspapers.com is a paid site, access to the Eagle is free if you access it through the BPL. There are a few functions that are only available if you register for an account with Newspapers.com, but that should be free, as well. You can read more about these features here. It looks like there's even an option to save the articles you find to Ancestry.com! (Newspapers.com is owned by Ancestry.com.) I don't have a current Ancestry subscription, so I haven't tried it out, but it seems like a helpful function.
The Brooklyn Newsstand's "About" promises to digitize other Brooklyn papers "in the near future," so there may be even more to come. (The lag between phase I and phase II of the Eagle digitization was quite long, so I'm not sure what sort of time scale is being referred to when they say "near future.")