I’ll second Canvas Craft. They do very nice work there. Might not be the cheapest. But the work will be done right and they will get you in and out in a day.
http://www.canvascraftinc.com/boat-covers-tarps-and-upholstery
You can do this 2 ways. Bring boat with cover on and then show them all of the areas you want worked on. Or, put the cover on at home and take some chalk and mark up all the areas you want repaired or reinforced. Then just drop off the cover.
Edit to update page link to the repar page:
http://www.canvascraftinc.com/canvas-repair
-J.