its a combo of all four. while the expereinces that I have are not while commuting, I still think they apply.

the fact that you are new certainly makes a huge difference. when I started riding, I was averaging 14-15 mph over 30 miles. I now can average 19 over 55-60 miles. your fitness makes a big difference. also, aerodynamics is important, I found that when I dropped the bars on my roadie an inch, I gained 1 mph average speed. thinner tires make for a faster ride becuase they can be pumped up higher, I run my 700x23's at 120 psi, and they are almost frictionless. the 27x1 1/4 on my commuter fixie only go up to 90, the difference is definitly noticable. plus, higher-quality tires will perform a lot better in the area of rolling resistance, and they are generally thinner. Lastly a lighter bike will make for a zippier-feeling ride, you can accelerate faster and climb a lot easier. manhatten is fairly flat though, so the climbing might not be an issue, but when you're sprinting to make that light, it might be useful to have a lighter bike.

all of the factors you named make a difference, however, if you are just commuting, i'd stick with the hybrid for a bit unitl your conditioning improves. set goals, ie, when you can average __ mph on your commute, you'll buy a roadie.