Police cornered and shot it full of sedatives near Holy Apostles Soup Kitchen, officials said.
Charlie Nuñez said police told him the bunnies can no longer live at the lot he manages.
Dorota Trec filed a lawsuit seeking the return of her rabbits.
Edward Nudel, 41, was charged with aggravated cruelty to animals, prosecutors said.
Dorota Trec, who owns nearly 200 rabbits, was taken into custody at the 68th Precinct, a source said.
Puppies were saved in 2010 after a fire and then last week from owners charged with animal cruelty.
The dog is named Oreo and was taken to the ASPCA.
The pooch, named Hennessy, has been taken to the ASPCA for treatment.
Police returned to rescue roughly 100 bunnies, days after seizing 74 rabbits earlier in the week.
Animal Care & Control is accepting donations of hay, supplies and money for the rabbits.
The dog was found on Jan. 22, 2015 in a Bronx dumpster.
The dog is now in the care of the ASPCA.
The Brooklyn DA is looking into the Third Ave. rabbits after hearing from an animal welfare group.
The dog was tossed from a moving car in Queens last month, officials said.
Jimmy Tarangelo's dog Spot was taken away from him and secretly euthanized over the summer.
Get our daily Afternoon News Update
Thank you for signing up!
Would you like to sign up for additional newsletters?
Thank you for signing up for additional newsletters.