You can also go to Novigrad immediately and swim through the river. However, the quests there are for higher level players, so it is not recommended.
I'm a bit paranoid about this as well...I can go to Skellige (im level 13 and the quest is level 16) because I want to go for Yen romance (that I want as my canon), but the 1 of 3 choices with the Baron to look for Ciri's whereabouts implies that I should go for Novigrad next because that's where he sent Ciri.
Does it matter in which way you finish the main quest? Or I can just go to Skellige without any issues and then keep Novigrad main quest for last? (of the 3 available).