I was down at urban landcruisers and saw a 60 with a moonroof, so yeah they are out there. I don't know if david( the guy that runs urban) did it himself or if it was a dealership job. If done right, there is usually not alot of problems and of course if you pay some jackarse 200 bucks to do it, you'll get rain on yer hed.
I would check to see if your local yota dealership does them. Thats probably a good start, and if not I'm sure they'll recommend a body shop.