Hm...does your boss and your company know what market rates are? Don't assume that your company is purposefully underpaying you; it may very well be that they don't know enough of the market. In that case, esp. if you're on good terms with your boss, it'd be a simple matter of educating them in your research.

Startups usually don't have a ton of cash, so if you feel like you're still being shortchanged and the company simply can't afford to pay you more (from the company's perspective, increasing your salary may mean increasing everybody else's as well), you can ask for other things: more options, more days off, better benefits, and as you mentioned working remotely.

You're in a good position, and have built up good will over the years, so I'm sure they wouldn't want to lose you. It might be just a simple matter of bringing it up, so do that first.