Second the omakase. Best thing to do is state your budget (we did $100pp for food, which left us sated, but not uncomfortably full, and very, very happy with our experience), mention any dietary restrictions (no beef, no pork, no sea urchin, etc), and let them take it from there.
I'd also suggest the same with their sake sommelier. She's both knowledgeable and very personable.
it appears that i am alone in this opinion given all the gushing about o-ya but... i didn't like it that much. the atmosphere was nice enough, the wait staff were nice enough, and the food was pretty good. my socks, however, were decidedly not knocked off. the only plate that really stuck out was the otoro - it blew me away. avoid the daikon dumplings - they were soggy and the flavors did not meld successfully. also the $9 house salad was a (very) small pile of shredded cabbage with a heavy slop of dressing - awful.
for the prices they charge, every dish should blow me away and the service should be impeccable. we had a back up of empty plates twice on a small bar with limited space in front of us and had to ask for another round of drinks twice. these may be small things but, again, given the prices ...