I am a 4th year now at NYCOM. I never did any fellowship. However, I can tell you that students who did an anatomy fellowship seemed to land better residencies. Of course, those same people had excellent grades and board scores. The neuroscience fellowship (2 people per year) only started during my first year at NYCOM. Therefore, it has yet to be determined how those students will do in the match. I am sure they will match extremely well. One know one of them personally. She was an amazing neuroscience tutor during the basic science summer program. It used to be that some gross anatomy fellows also had duties as a pathology or neuroscience fellow. That was until they split the fellowships apart.
I know that past anatomy fellow have rountinely matched into radiology (e.g. Stony Brook, Mt. Sinai in Miami), orthopedics (osteopathic), and many of them of them go into excellent general surgery programs. I would say that anatomy fellows seem to match better than OMM fellows. The OMM fellowship is a big bonus if you want to go into a field like PM&R. Those fellows have match into excellent PM&R programs like Harvard/Spaulding. But, even people who haven't done a fellowship matched into excellent PM&R programs. Otherwise, I really don't see the OMM fellowship giving you a leg up in landing better residencies. It is more for educational and hands-on experience.
Go for the neuroscience fellowship if you're willing to spend an extra year at NYCOM.