Maybe a day late, but I guess the place I've been going to for decades is Top Dog in Berkeley, California. It's gone through locations that have come and go as well as at least one franchised location. However, the ones that remain are operated by the original owner. He's got libertarian leanings and the walls are covered with various libertarian writings.
Pinks seems to have a following around Los Angeles. I haven't been there, but I did see their location at the Unversal Studios Hollywood City Walk.
I guess there are the national fast food chains that have hot dogs like Sonic Drive-In and even Burger King.
Strangely enough, I think the biggest seller of hot dogs in the US is probably Costco.