Steve,
I've only been through the Dallas MEPS, so I can't tell you any specifics about NYC. But I can give you an overall idea of why the big, long wait.
I'd follow your OSO's advice and get there by 0500. That should be plenty early. I waltzed into the MEPS at 0545 and got stuck behind a lot of kids going in as enlisted - they lined them up in groups to go in. Thankfully for officer candidates they assume you can find your way and they let me cut in front of them to get through the door. Some stuff you can get out of the way pretty quick - i.e. blood pressure, pulse, eyes, etc. However, I had to stand in line like everyone else. I told them I was there for a commisioning physical and they just gave me a blank look and told me to stand in line. The hearing test takes a lot of time because you have to wait outside for two or three cycles before you can go. Also, everyone has an interview with a doctor after the majority of the tests are done. There are only two or three doctors for a group of 50 - 100 guys. There are two areas that bottleneck and cause the most time. They gather everyone in a room to fill out paperwork and take a breathalyzer test - you have to sit and wait for them to fill up the entire room. Of course there are always the morons that have a question for everything so that takes even longer. Then there is the agility tests and the infamous "duck walk". They again gather you up in a room. People come in in ones and twos from the other stations, so it is another good wait before they even start.
Then after all of that you have to wait for them to sign off on your file and call your name - which takes another good long time.
Bottom line is that this is a government run facility - meaning they will get to you when they are good and ready. Don't expect any special treatment as an officer candidate - they'll just put you in with everyone else. Your experience, or for that matter - others on this forum, might be different - you might luck out and there might not be that many people going through MEPS that day. The people there might not screw up your paperwork. They might give you special priveleges as an officer.
The problem, though, is that is a lot of what if's - I'd go in there with the idea that there will be long lines and it will take until noon. That way, if it isn't the case you will be presently surprised, and if it is the case you won't be pissed like I was the whole time.
Long answer. Hope this helps.