1. 화장실 means powder room.
화장 (make-up) + 실 (room)
And it refers a toilet in common whether it's for public or not.
2. 목욕실 literally means a bath room.
목욕 (bath) + 실 (room)
And we don't use it much and when the time comes to use this word, it usually means a private bathroom like installed in residential houses.
3. In addition to these words there is a word for a public bathroom in Korean. And it is 목욕탕.
목욕 (bath) + 탕 (originally means "boiling" but in this case it means "hot tub" with boiling water in it.)
It is a spa including sauna and other body care & relax facilities.