I've been to all 3 recently. They were each fantastic in their own way. Overall, I'd rank (1) EMP, (2) Daniel, and (3) Bouley. EMP's Gourmand menu is terrific- courses just keep coming, and it was one of the few where I genuinely liked every course and some were outstanding. Daniel's tasting menu was also very good, the entrees were particularly delicious, but overall it had less WOW factor. Also, I thought the service was better at EMP, very good descriptions of each course and the accompanying wine pairing, whereas Daniel seemed somehow less professional, but maybe it was just an off night. The Bouley lunch for $48 is I think one of the best deals in the city. Atmosphere is also great, more intimate, french, whereas both EMP and Daniel are very grand but more cold. Outside of that, I think the food at Bouley was all very good, but kind of standard and unexciting compared to the other two.
If you haven't done the EMP Gourmand, I'd say go back and do that- otherwise Daniel is definitely worth a try, and Bouley is great, especially at lunch.
When you were at EMP in December, did you have the Gourmand menu? If not, and you decide to go back there, I highly recommend it because it is super-duper--sensational -- one of the best tasting dinners we've ever had!
I can't comment on Bouley since we've never been there, but we have been to Daniel a few times, and if you want to try something new (to you), I certainly think it's a fine choice.