One problem with gardening in the city is the likelihood of your soil being somewhat toxic. There are simple tests for this that you can buy online, as well as services that you send a sample away to in order to see what's going on. Here's a great article with a few tips on what to do if (or in Brooklyn, when) your garden has a bit too much bad stuff.
My garden is toxic!
Before I planted my garden, I spoke to a botanist friend who had some of the same recommendations as in the article - plant fruit stuff in the toxic soil, and leafy stuff in raised beds - so that's what I did!