Well established, reputable roofing contractors. Get more than one estimate. Ask friends, family, co-workers for referalls and ask the roofing contractors for references. You can also ask them to give you adresses of recent projects so you can see their work. Make sure they are licensed and insured and will back their work in writing.

Make sure they do a good job with the flashing around the skylight, as that can be a key source of leaks.