While exercising your right to protest is admirable, there are other more effective methods to consider. While the VIPR teams may be authorized and financed by the federal government, they are not law enforcement. As such, they require the active cooperation of your transit police, your municipal police, and your state police to carry out their warrant-less searches. (The FBI and federal marshals have better things to do, really.) Without the authority to stand around in a fake badge and remove naysayers from the premises, just how effective can VIPR be?
So talk to your city council representative. Be polite, presentable, and logical. If you're lucky, you might be able to make a presentation or get a sponsor on some legislation. If you can get even a small group of people together, your chances of success will improve. Your state or city may give you some additional tools with which to affect change: Initiative and Recall. Use them.
While the 4th amendment is nice, in principle, that's not what is going to get the attention of your city government. Focus on the fiscal impact of the TSA's presence. How much time does the MBTA police spend assisting the VIPR teams? Does the city need to hire any staff to support them? If just one staffer has to spend ten minutes of their day dealing with this stuff, the TSA's presence is not revenue-neutral. Even if you can't get these numbers, bring it up. It will get them thinking, if nothing else.
Focus also on the impact on commerce. Does the TSA delay trains, or make people late for work? Does the TSA significantly reduce the number of riders on the subway and put them on already-congested roads? Point out the potential for theft and harassment—there have been a number of news articles about this very topic. Once that is finished, all you need to do is prove that the TSA does not actually increase security. Bring in expert testimony, if you can get it.
Once you have proved that VIPR is unpopular, decreases city revenue, negatively impacts commercial interests, and is disruptive to the public order (i.e., "don't grope me"), you will have lots of momentum behind a city ordinance. The goal of the ordinance should be to (1) prevent any municipal law enforcement from cooperating with these searches, and (2) actively remove anyone conducting such searches from the transit system. In the absence of any overriding law, city ordinance prevails and—good news—it's an election year.
VIPR will, having been removed from the city, need to spend time, effort, and money passing overriding legislation. If you're lucky, they'll just go away and find someone else to tyrannize. Even if they don't go quietly, the REAL ID Act is a great example of what states can do to a federal program if they refuse to support it. So go ahead, take back your city.