Exercise #2 Wins.
Prone is the way to go (Y's on a swiss ball would be ideal).
According to Maenhout et al 2016, the highest middle trapezius and lower trapezius muscle activation was found in prone exercises.
Note:
Exercise #1: Typically the upper trap overpowers the middle and lower traps since it's commonly too strong and hyperactive.
The middle and lower trapezius however, are still very important during overhead exercises to promote optimal mechanics.
It's important to learn how to activate the low / mid trap as a
stabilizer, rather than a mobilizer, during overhead shoulder
movements.
That's were the Prone Y's come in -- they will help accomplish this (strengthening while correcting dysfunctional firing patterns).
Source: https://www.ncbi.nlm.nih.gov/pubmed/26894494