new roof + new skylight windows
Almost all sky lights on a roof are mounted a 2x3 or 2x4 curbing that is nailed down to the roof sheathing. Flashing metal pieces are the bent up and nailed to the outside of the curbing and put down under each succeeding tier of shingles. The skylight generally us sized to fit on the top of the curbing and has a flange that comes down along the side of the outside of the curbing. The flange should come down far enough so that it fully covers the top edges of the flashing metal pieces that come up along the side. 

As the roofers are already up on the roof doing work around the skylight it should be a piece of cake to have then install the new skylight. Mounting is typically as simple as nailing or screwing through holes in the side flange into the side of the curbing. Having the roofers do the job allows them to remove the old one and give then the correct access to install the new flashing metal as then shingle past the opening and curbing.

Another significant advantage is that it keeps one less person or group of persons off your roof that could do damage to your new roofing.