It really depends on what insurance you have, there are many GIs in NYC that do not take insurance.
Making a generalization here but the best GIs in NYC are associated with University Hospitals like Mount Sinai, Cornell Weil IBD center and Columbia.
You will get the best care at these Hospitals and the GIs associated with them, they have the most resources and typically the best training and experience.
Drs Present, Marion and Chappman are probably the best known GIs in NYC and they are associated with Mount Sinai. They also do a lot of Clinical Research at their practice
www.ibdgi.net .... I used to go to their practice but the GI that I have used for the last 7 years (dr Steinlauf) recently moved from their practice to the Cornell Weil Center. I definitely recommend him and he takes all types of insurances now.