If this is true, then the rational position would be to assume that the government may or may not be lying to you. Which is what I believe.
"'The government' is hardly a single entity."
The people are different, but if the Milgram experiments (and sociology in general) have taught us anything, it's that a person's social influences are as important to their decision making as their intrinsic character. And the laws, rewards, and punishments are largely the same across departments.
I realize the EPA is different from the FDA. However, the reasons why the EPA buried studies about the amount of mercury in freshwater the day before issuing new guidelines on acceptable mercury levels are largely the same as the reasons why the FDA approved OTC plan-B only for women 18+.
The takeaway is that bad things don't (usually) happen because of bad people. They happen because organizational behavior, psychology, and sociology allow us to make an educated guess that if an organization looks like X, then what tends to happen will be Y.
Now if I see patterns across organizations that you don't see, maybe that makes me a conspiracy theorist and maybe I'm seeing patterns that aren't there. Or maybe I just see patterns that you don't see.
I agree that at the end of the day you have to think about these problems individually for yourself. I don't actually believe the vaccines are all that dangerous, but at the same time I'm not going to take them just because the CDC or NIH or whatever say they are safe. The reason is that the people running these departments are operating under largely the same structures and incentives as the people running every other government department, and history as a whole shows that these sets of structures and incentives tend to produce unsavory behavior.
Sounds like you're saying "don't trust all your decisions to the government", which is trivially true and apropos of nothing.
1) This has everything to do with pseudo-science. There are no credible studies pointing to ill health effects outside of extremely rare cases in which a person is allergic to some part of the vaccine or has some other pre-existing condition. And there are numerous studies indicating that you're more likely to get struck by lightning than to have any reaction to a vaccine, outside of a sore arm.
2) "The government" is hardly a single entity. You're displaying conspiratorial thinking here, which is pretty tough to take seriously. You're discussing the EPA and NY city government, which is not the same as the NIH and CDC. Additionally, it's not only the U.S. government which is strongly recommending these vaccines. If you'd like to continue that line of argument, you'll have to take it up with probably every single first-world government.
3) Being an intelligent and rational person means evaluating claims individually, regardless of the source. Starting from the position that the government is lying to you is just as stupid as assuming they're always telling the truth. Of course there are fuck-ups and cover-ups, but that doesn't mean everything is.