Depends on how long you'd plan to keep the new wheels and how many miles/sets of tires you'd put on them during that time. My choice would probably be to go with 700c since I'd plan on keeping them for at least 50,000 miles and probably go through 10 sets of tires so the greater tire choice would win out. And I'd also keep the old set of wheels/tires around and plan to use them during the winter/rainy season and as emergency spares if something breaks in the new wheels (I presume your brake pads have enough adjustment for both sizes).
Ironically, as a result of poor pre-trip checking, I found myself looking for a replacement tire on a short tour just a couple weeks ago. The only bike shop in town was closed that day so I checked at a discount shop. They had several tires in the 26" size (not surprising), and also had one in 27" - but none in the needed 700c. Fortunately my tire survived another 50 miles to the next town with bike shops.