There is a park in Yokohama called "minato no mieru oka koen" which is famous you can see beautiful night-view of MinatoMirai in Yokohama. Many couples go there to see night view to confirm their love. I recommend to go there at night time when yokohama seems like a tons of stars with thier lights.
How about stay at a nice hot spring hotel on a mountain side with a private scenic hot-tab attached to your room and propose at sunset?
How about observation deck in Roppongi Hills.
The view from 250m above is astonishingly beautiful and romantic, that no one would decline marriage proposal here!