Well... the thing is, people will always think they're being unfairly targeted. But its far more likely that the cyclists are in fact breaking the law. This is generally a problem, since cyclists have developed (this is a "we" statement, I don't want to sound like I'm not including myself in the cyclist subcat) an attitude that they get shat on by society constantly, they tend to get more upset when they're ticketed, and yet someone else isn't.
When a police officer pulls someone over for speeding for example, you'll not need a keen eye to notice that they likely weren't the only one speeding, so why are the other people not being pulled over as well? This is where being a mature adult comes in... as there's no "but they did it too" argument once you're over the age of 14.
All of that said, its very likely that the police are targeting cyclists. They (the police) know the city better than almost anyone, and I'm sure they've seen a relative population explosion in cycling on the last 5 years. Part of this is because people are getting into cycling for transportation in our generation more and more, but a much larger part of this is probably because "fixies" if you will, have become trendy. These "fixie" riders are the ones I envision as the main problem here, since stereotypically, they are the "anti-authority" type (how do you say hipster nicely?). More than that, they're probably riding ill equipped and downright dangerous bicycles (brakeless fixays, or improperly lit fixays). Thus setting them up for ticketing... see the cited law posted at the end***.
That said, "targeting cyclists" is no different than setting up a speed trap? If you choose to break the law, then you should be prepared to face the consequences? I feel like its that simple?
As you said though, it is difficult to know without being there. My good friend Carolyn is living in NYC now and she was an avid casual cyclist (read hipster wannabe)... I haven't heard anything from her, but I'm not certain if she's gotten up to the skill of riding there yet...
And lastly, the state (starting with the city) is bankrupt. The police want to keep their jobs. They're going to be "cracking down" aka earning their keep. But if you're following the laws, I don't see how they could have any reason to stop you?
***From the NYS Vehicle and Traffic Code.
§ 1236. Lamps and other equipment on bicycles.
(a) Every bicycle when in use during the period from one-half hour after sunset to one-half hour before sunrise shall be equipped with a lamp on the front which shall emit a white light visible during hours of darkness from a distance of at least five hundred feet to the front and with a red or amber light visible to the rear for three hundred feet. Effective July first, nineteen hundred seventy-six, at least one of these lights shall be visible for two hundred feet from each side.
(b) No person shall operate a bicycle unless it is equipped with a bell or other device capable of giving a signal audible for a distance of at least one hundred feet, except that a bicycle shall not be equipped with nor shall any person use upon a bicycle any siren or whistle.
(c) Every bicycle shall be equipped with a brake which will enable the operator to make the braked wheels skid on dry, level, clean pavement.
(d) Every new bicycle shall be equipped with reflective tires or, alternately a reflex reflector mounted on the spokes of each wheel, said tires and reflectors to be of types approved by the commissioner. The reflex reflector mounted on the front wheel shall be colorless or amber, and the reflex reflector mounted on the rear wheel shall be colorless or red.
(e) Every bicycle when in use during the period from one-half hour after sunset to one-half hour before sunrise shall be equipped with reflective devices or material meeting the standards established by rules and regulations promulgated by the commissioner; provided, however, that such standards shall not be inconsistent with or otherwise conflict with the requirements of subdivisions (a) and (d) of this section.