Yes, there is a pump out service that you get at the marina included in your dock fee. You can schedule for every week or whatever you need any they come around based on your schedule.
Have you considered simply looking for a cheaper apartment? You can prob find a place for around $1000 nowdays. You're currently being ripped off. You can even try to negotiate with your landlord to lower your rent. Otherwise, just bounce, telll him you got laid off, can't pay next month's rent and are leaving the city.
$1000/month rent is simply not possible in NYC. A boat might be ok but the ones in the Hudson River marina on west side of Manhattan (near where the jet ditched recently) were grandfathered in. No more room at the inn, I believe? I doubt a slip is available until you go out to Queens, down in Sheepshead Bay area or over in Staten Island or Jersey. Other than a lifesytle change (boat or RV) I don't think the numbers warrant a move. As far as safety and secuity there are pluses and minuses to living in the big city or living in the boonies. It all comes down to personal preferences.
I knew an opera singer who used to drive to most of his east coast and midwestern gigs in his RV, he saved the money that he would have spent living in a motel for 2-3 weeks at a time and enjoyed the people he met and often entertained in RV parks.
$1000 a month is just not a workable deal in NYC. If you're paying $1000, you're either in the ghetto or commuting so far that it's just not worth it anymore. I've given up on cheap apartments. They've got roaches, negligent landlords, etc. In my building, the landlord more or less knows that most of us make money and treats us with respect. Compare this with my WaHI experience where the guy was basically a slum lord. Living with other people is just not feasible. I've got too much going on to deal with other people's crap. Renting rooms subjects you to the owner's wrath and privacy is never quite there. There's a peace of mind premium I am wiling to pay for apartments, even though I'm clearly looking at alternatives that can give me peace of mind, possible escape, and save money. Frankly, I've had enough of other people. I'm 29, I'm done with that roommate crap. The girlfriend is the only one I'd even consider.
Check craigslist, it's 2009 not 2007. Won't be long before $1000 apartments become the norm. You can already get decent ones for $1200 in one of the good neighborhoods of NYC.
I would look for the small manufactured house or even mobile home to rent instead of the boat aka hole in the water where you pour money. Instead of RV, consider a travel trailer. There must be some homes for rent as snowbirds going to the South for the winter and maybe don,t want to return if someone rented their NY state house .