You need a lawyer - this is not a self-help situation. Your local and state bar associations can give you a referral. If you cannot find a NYC attorney that also practices law in Connecticut, you should be able to get a referral to a CT attorney.
If we do not have a signed fee agreement I am not your attorney and this is not legal advice.
You do not state how someone living in NYC could have their animals seized in CT, or why the animals were seized and charges brought.
The bottom line is that you will need an attorney - one in CT, where the trial will be held. Contact the CT and the relevant county's bar associations for referrals.
The foregoing is for general information purposes and does not establish an attorney-client relationship.
A skilled and experienced attorney can present your evidence to the prosecutor and attempt to get this situation straightened out. You shouldn't try and handle this on your own. I recommend Attorney John Thygerson, who can be found here on Avvo, and through his website, I've put in a link below.
This is general advice and does not establish an attorney-client relationship.