--I want to shell out for the quality track frame, but I'm thinking that anything shiny will be stolen. Steamroller or Marushi gas-pipe chipped-paint 10speed conversion?
--Are theives savvy enough to recognize a carbon fork?
--If I use 700x28s, will thieves think that it is not a "racing bike?"
IMO, you should get the bike you want to get. Don't start off in this city "hobbled" in some way. You just have to be smart about how you go about presenting and securing your bike. It can't be too much diff't here than Philly...people round here will take anything that ain't bolted down. Good components, bad ones, racing bikes, rusty touring bikes, even kiddie bikes. Don't let the fear of theft dictate you into short-changing yourself on the bike. Get what you want, just be safe and smart. Of course, if you're gonna be in a position where you live/work in a particularly unsavory area, you will want to heavily consider options.
--Same question, but for Suzue Promax/Level hub on one hand, or el cheapo track jr hub on the other?
You're putting your bike to the test. The conditions can be rough. Don't skimp on the hubs!
Ride-related:
In philly, I've happily rocked a 39x13, giving 78 or so gear inches. Philly is stop and go, but with lots of places where you can/have to get going fast, and some hills. Should I down gear some for NY?
Depends on how you ride. You can keep your gears and still get around the city just fine. On the average riders I talk to are in some similar 70's-low 80's range...