I have been traveling to/from NYC from Boston for the past two months, and feel it's important for business and pleasure travelers who will arrive at the LGA Marine Terminal and want to get a car rental.
I have been loyal to Hertz for the past few years. What I have found is that 1) Hertz shuttle service to/from the Marine Terminal is an afterthought and reliably unreliable in terms of time, especially at pickup and 2) service at this Hertz location is highly variable.
Pickup, for example, involves waiting at a bus stop for almost always over 15 minutes, and sometimes longer than 30 minutes, for the shuttle to arrive. During the winter this becomes a "manly man" activity as you begin to understand what Valley Forge must have been like as you stand in the biting cold waiting for an indeterminant time period for the shuttle to come around.
When you drop off your car, and you want to go to back to the Marine Terminal, do NOT just get on the any terminal shuttle. Oh no. You need to go inside and ask for the "Marine Terminal Shuttle," and then go wait 5-15 minutes for the thing to arrive. If you do get on the regular terminal shuttle (been there, done that), you will be told as the shuttle drives past the Marine Terminal and arrives back at the rental center that your driver advised you that the regular shuttles do not go to the Marine Terminal. I'm sure that they do, but I have yet to have heard anything intelligible from the drivers while on these shuttles.
In the end, most of my colleagues rent from Avis and don't have these issues, and I always see an Avis shuttle outside the Marine Terminal ready to go (usually while I am freezing to death at the bus stop). So if you must rent a car while in NYC and arrive/depart from the Marine Terminal, you might want to try Avis.