How far is Bed Stuy from the Flatbush/Ditmas area?
There are a few good places here. One "off-the-beaten-path" kind of choice is Andrew's, on the corner of Church Avenue and Coney Island Avenue (right off the B35, a nice walk from the B/Q trains to Church Ave). It looks like a dive and there's only counter seating, but the home fries there are the best I've had. And? With coffee and juice, you'll leave having spent under $15 for two. I swear.
In Ditmas/Flatbush there's the Farm on Adderley on Cortelyou Road, a place with fabulous brunch and a seasonal menu, and Picket Fence, also on Cortelyou, with nice comfort foods. These are also near the B/Q.
Apt. 138 (is that the name?) on Smith Street has a nice breakfast menu (it's right off the F train) ... A lot of those little restaurants on Smith have great, inexpensive breakfast/brunches. (Boerum Hill Food Company is another I've tried.)
And, if you do want to trek to lower Manhattan, Zucco's on Orchard Street ("le French diner") makes incredible French breakfasts, including fabulous French toast and something called "Le Brique de Blyda" (I think that's the spelling), which is a phyllo and goat cheese confection atop ratatouille topped with a poached egg. Yum.
Hope that helps a little!
Breakfast tends to thrive in neighborhoods where people don't work (because it's beneath them). I'd suggest a bus ride or G train trip up to Greenpoint or Williamsburg; you can try Diner, or Brooklyn Label, or Egg, or that place I like on Bedford Ave and N 9th with the amazing oatmeal.
The food at Tom's on Washington Avenue in Prospect Heights is not as welcoming as the atmosphere, but the pancakes are probably what they do best. May want to bring your own coffee, though.
If you're willing to go into Manhattan, Shopsin's is up and running at Essex St. Market. If you're interested in bread pudding french toast, with cheddar cheese and sausage mixed in, and served with real maple syrup--maybe you should check it out.