Start with subtle clues, slowly becoming more direct.
As is commonly advised to writers; show, don't tell.
People like making decisions on their own, but they also generally want to make others feel good. And especially in new environments and situations, we mimic. It's all about gradually going from subliminal cues to explicitly stating the intended outcome.
1 - Take off your own shoes.
If you're bringing guests to your home, take off your shoes first, and then your coat after. This gives your guests the time to see that you're taking your shoes off, and they can follow suit. People generally take off their coats first and then their shoes, so it might feel weird to do this order, but it also draws extra attention to the act.
If you're already at home wearing nothing but socks (well, hopefully a bit more..) you can't really take off your shoes, so skip this bit.
2 - Have a place for the shoes
Like others mentioned, having a shoe rack would be very beneficial. People see they that shoes are kept near the door, so they're likely put on/off near the door. They can then infer that they should do something with their shoes after using the door. As they're currently wearing shoes, the logical option is to take them off.
3 - Suggest where they can put their shoes
If you're not sure they've seen the rack, or if they're not preparing to take off their shoes, point the rack out, in a non-intrusive way.
"The coatrack is there, and you can put your shoes underneath"
This way they definitely know where to put their shoes if they decide to take them off. You're implying a link between hanging up a coat and taking off shoes. They're currently taking off coats, so perhaps take off the shoes too?
The phrasing here is important. When you say "you can do X" it still leaves the decision up to the guest. You're not telling them to do X, you're assuming they want to do X, and helping them do it. it's supportive and guiding, not instructive and authoritarian.
4 - Outright ask them. But be kind.
When they don't get any of the clues, ask them if they want to take of their shoes. Don't tell, ask. "would you mind taking off your shoes? I like to keep the house clean." It's still not authoritarian, but a request, still technically leaving the choice with your guest. But if they're nice people, they'll comply.
Because they're visiting your house, they'll likely act nice. They're probably there to connect closer with you, which doesn't work if they frustrate you. Second, it's your house, your rules, at least that's the social contract in most cultures.
5 - Put your foot down.
Oy bruv take them trainers off before I knock you in the gabber. I'mma screw you right up mate, loose the boots. Respect my authoritah!
I kid, I kid. Don't actually get aggressive.