It depends on what you are looking for. I would go along with Highlander Daz if you want to walk out of the shop with a kilt. Armstrongs in the Grassmarket have lots of second-hand kilts (mostly ex-rental) and you should get something to fit although you may not get the tartan of your choice. Their prices are £60 upwards (I think) They also do lots of jackets for around £150. They are all "proper" kilts not the cheap & nasty stuff in the "Heritage of Scotland"/"Pride of Scotland" shops (they can be recognised by the turban-wearing staff). If you want to get properly measured and choose a particular tartan for a top class, perfectly fitting kilt that will take 6-8 weeks to make then I can only recommend Stuart Christie in Queen Street who will charge around £400.
There are still a few genuine kiltmakers on the Royal Mile and McClef's suggestions would also be mine although I have never bought a kilt from any of them but Hamish speaks highly of GT. The "Edinburgh Woolen Mill" now seems to be owned by more of our friends from the Indian sub-continent so I would carry on walking past.