There are no roof rack manufacturers that have a system compatible with your 2007 Nissan Frontier truck's cab roof. However, a truckbed rack system is a superb option. You will not be able to use a tonneau cover in combination with a truckbed rack however.
The Yakima Outdoorsman 300 (compact size) truck bed rack system is an excellent set up for carrying a canoe on your Nissan Frontier. The Outdoorsman Towers come as a half set so you will need to get two half sets of Outdoorsman 300 Towers to make a complete set of four Towers for the front and rear of your truck bed. You will also need to get a pair of 58 inch cross bars to use with the Outdoorsman Towers (this length is necessary to span across your truck bed, however you can select longer crossbars as well). You can then connect the Yakima Gunwale Brackets canoe carrier directly to the two cross bars. Simple to install with no drilling required. The Towers quickly clamp onto the bed siderails.
Yakima Outdoorman 300 truck rack video
http://www.orsracksdirect.com/yakima-racks-outdoorsman-truck-rack-video-demo.html