I had a brake master cylinder go bad in my old integra and had similar symptoms. It would work w/out a problem for awhile and then next stoplight I'd have to pump the brakes like crazy to get her to stop then it would work fine again. also leaked out of the back of the MC where the pushrod was. If it turns out to be your MC going bad carquest, if you have them in your area, sells the remanufactured ones that are original equipment-Nissin, for right at 200bucks. Not terribly hard to replace yourself if your a fairly handy person. Good luck on tracking down the problem man and be safe untill you do. having no brakes when you step on the pedal can be damn scary.

but like the other guys said definitely try replacing the fluid and getting the air out of the lines before you buy a master cylinder.