I realize I am probably too late with my response for this ride, but you can keep this note for the future. First, the Bay ridge part of the greenway is is really nice and in good shape, but if it is windy the wind can be much, much stronger along the shore. Once you past the bridge, the roadway gets progressively worse and bumpy. As you approach Bay Parkway, stay to the left, then don't worry too much as you ride the service rode. Once past the shopping center parking lot, it is pretty clear and easy riding until you get close to the Cropsey Avenue exit. I usually stay to the right and go down closer to the Home Depot before heading left to Cropsey. You make right on Cropsey and then I recommend that you stay right as you approach a large intersection (Neptune). You can go straight across Neptune to Coney Island, but I would recommend that instead you make a right on to the bike lane on Neptune and take it all the way to the end at Sea Gate (which is a gated community, which you can't enter). However, once there make a right and go up and explore the small area just north of Seagate, then double back along the Bay (great views of the Verrazano) the few blocks back to Neptune and then head on down to the Boardwalk. Take the Boardwalk through Coney Island and Brighton Beach to the end, go up a block (I forget the street's name) and make a right go over a block to I think Corbin and make a small right and then a left on to Oriental Blvd and take a ride out to the end of Manhattan Beach, then make a left and go back up to the inlet of Sheepshead Bay, make another left and ride along the water back to West End, make a right and right past the inlet a quick left on to Neptune, which you can take back to Ocean Parkway and then a right on Ocean Parkway and head north.
I often do this ride adding lots of variations.