Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Rochester to Williamsburg as you normally would.
For a flight from Rochester to Williamsburg, you will be flying from Rochester. Rochester (RST) is just 7.0 mi from the center of the city. Rochester is the only Rochester airport and it handles 0 outbound flights to Williamsburg per day. 2 airlines have flights to Williamsburg from Rochester on a regular basis.