I'd say Gjelina. It's a little different than the other restaurants that are open late since they serve a different, smaller (and not as interesting) menu after a certain hour. Getting a reservation for the regular menu has been the toughest for me
It depends on how much you plan in advance. Ink uses OpenTable, and even now I can get a table for 4 at 9:30 PM tomorrow night and at 10 PM or 10:15 PM on Saturday night. Not necessarily optimal times, but doable.
I've had good luck as a walk-in to Son of a Gun every time I've gone (haven't had the foresight to make reservations). Agree on all the others and will add Pizzeria Mozza and Angelini Osteria from my own experience.