There are typically 2 factors to consider: distance & safety. In regards to distance, I would recommend staying no more than 6-7 subway stops into Brooklyn from Manhattan, depending on the line. Anything further out will make a trip into Manhattan at least 30 minutes.
In regards to safety, areas like East New York, East Flatbush, Brownsville, parts of Bushwick, parts of Bedford-Stuyvesant (Bed-Stuy) and parts of Crown Heights all have high crime rates.
You can also add demographics to consider, but Brooklyn is all about diversity, so I'm going to recommend you embrace that...it's part of what makes Brooklyn special! about 6 years ago