At that time of night, I'd definitely take the boat to MK from Poly. The boat will be packed coming FROM MK to the Poly, but you should have an uncrowded trip TO MK on the boat. Most people will get on the monorail. The monorail tends to have its worst slowdowns, etc. at around park closing. Also, the boat docks at MK are slightly closer to the resort buses than the monorail, and the Poly boat dock will be closer to where you watch Wishes from than the monorail stop at the Poly.