Went there this past Saturday prior to theater. Taken right away for our 6PM reservation (8PM show a couple blocks away).
Possibly our 2nd or 3rd best meal in NYC, and we dine out in the city at nice places 8-10 times/year (definitely behind 11 Madison Park a few years ago, we're debating 2nd and 3rd). The space is lovely, the service was incredible, and the food was just delicious.
Started with the deviled eggs and croque-madame. She had the veal meatballs and I had the schnitzel. We had the side of broccoli and garlic (amazingly good!), and finished with the banana pudding.
Also ate at Minetta Tavern and Quality Meats over the weekend, so a delicious time was had by all, but Commerce was just outstanding.
I thought the chicken was pretty good. It's really a large bird -- ended up taking most of it home and got at least 4 more meals out of it. It doesn't need to be ordered in advance, but you should let the restaurant know as soon as you sit down so they can get it started.
Don't know about them running late. If you like offal, their ragu of odd things is great. And make sure you save room for their wonderful bread basket.