There are tons! Some of the most famous ballet companies are based in New York City, including American Ballet Theatre and New York City Ballet. Both of them usually perform at the Lincoln Center which is in Manhattan.
There are also many smaller ballet companies that are based there such as Complexions. The smaller ones are usually more contemporary, and sometimes even considered modern, but there are many others. Speaking of modern, there is also Alvin Ailey.
Anyways, check out the websites for these companies, and depending on when you’re there, they may have some performances going on. If not, check out some smaller theatres like the Joyce theatre, because many companies also tour to New York City to perform. Have fun!