Krabby Patties are your average fast food burger ala Quarter Pounder, Whopper, etc. They aren't that great, not everyone likes them, but enough people do like them that they've created a successful business. Despite what Spongebob puts into them, including the "secret recipe," they're meant to be mass produced and cost effective (much like Big Mac and the Mac sauce.)
Bob's burgers, on the other hand, are personally crafted. He grinds his own meat, uses fresh ingredients, and cooks each burger individually, which is why they have a better taste than your run of the mill fast food one. They're juicier, thicker, and put together better than an assembly line.
That being said, they still appear to be a simple burger, sometimes with an extra ingredient based on a pun, like kale. That's why you can have Bouchard say they're really good, but Benjamin think they're still pretty average.
What would I rather have? Probably a Krabby Patty just on the idea that it's an iconic burger and to see what it tastes like. Bob's burgers are great, but I can get a great burger any place. I can only get a Big Mac, for example, at McD's.