Come to think of it, the last level of the Local Leader perk does explicitly say that "you can now invest 500 caps with vendors" or something along those lines. It's possible that this is some kind of glitch, because I didn't see any change after getting that perk.
edit - A quick search led me to this Reddit post.
https://www.reddit.com/r/falloutsettlements/comments/3tkh62/how_to_upgrade_your_shops/
They're basically saying the when you go to the barter menu, there's an option to "Press Q to invest."
And I just stopped in the middle of typing this post to check, and the option is indeed there. I just invested 500 caps with Anne Hargraves, the legendary clothing vendor. I'll do the rest tomorrow. Open the barter menu and there are all of the different options along the bottom below the inventory screen. The last option is "Q: Invest" If you're on console it'll obviously be a different button, but it should be there, assuming that you have the Cap Collecter 2 and Local Leader 3 perks anyway.
So there we have it. You can invest an additional 500 caps into each of your stores. According to what I'm reading, you can also invest 500 caps with Trashcan Carla and the various merchants at Diamond City, Goodneighbor, and wherever else. I'm about to head to bed but I'm going to have to look into that tomorrow. I've got enough caps to invest in every merchant I visit regularly and still have tons left over, so that would be a worthwhile investment with my water farming and mass-production of Jet.