79th street basin has moorings but availability is definitely an issue and you need a
tender. I think there is also some transient
dock space but it's pretty expensive, if available. You might also consider City Island, up in the Bronx, where there are some very nice marinas with tender
service, but the problem there is that public transport via bus and subway to Brooklyn will take a couple of hours. City Island is a fun, funky place to visit.
The City also operates World's Fair Marina in
Flushing Queens, not far from LaGuardia
airport, but public transport to Brooklyn from there is probably as bad as from City Island.
I think your best bet might be to park your boat in one of these three South Brooklyn spots: Gateway Marina (dock space), Miramar YC in Sheepshead Bay (guest mooring/launch
service or maybe dock space) or Sheepshead Bay YC (guest mooring/launch service). None of these are close to subway but there are bus links (very slow) or you could always call car service (taxi alternative) for a quicker ride to the subway than using the bus. There are multiple car service outfits and you could try to strike a deal with one for regular daily subway roundtrips.