Both places are extremely cold in winters but if you want to go with the flow of bhagirathi river then harsil will be the better option for you... otherwise munsyari have its magic too.
Munsiyari because Harshil people have migrated to Uttarkashi and only Army will be there. You will also face problem of food and stay. From Munsiyari you will witness the beautiful Panchachulli peaks.
Both the places are wonderful to visit. In Munsiyari you can see beautiful hill, great Pancha Chuli peak, and can visit to the Birthi fall, Khaliya Top, Maheshwari Kund, etc