My sister lives with us because she's chronically ill and she often can't sleep at night because of her illness. She's often too weak in the mornings to do much when he runs around in her sleeping area turning on every light and the television as loud as it will go and since I work from home I'm not always attentive when he does this til it's too late. How can I make him stop doing this? I know it's worsening her condition with her multiple disorders to be awakened like this when she's already awake through the night. Sometimes he wakes her up to insist she play with him and she feels guilty that she can't get up to do that. There's nowhere else she can live because we don't have other family or money to have her anywhere else.
Five years old is old enough to have some sense of boundaries, but it's not surprising that he's trying to get your sister up. He can't really understand what she's going through medically, and if he doesn't have a sibling or someone to play with, of course he wants her to get up and play with him while you're working. Kids need socialization - it's hardwired into them.
Assuming you don't have the option of getting him someone else to play with, sending him to a friend's/family member's house, then what I'd do in this case is focus on schedule. It sounds like it's 9am and you're "at work" and he doesn't have something to do, so wants someone to play with. Set up a schedule where you have specific activities he can do at various times, and set up a reward system where he gets rewarded for sticking to the schedule. Then, start this on a day where your work is maybe a little lighter and you can help him stick to it.
It won't help instantly, but if you get him used to the schedule, it should help. I wouldn't expect it to work perfectly every day - but if it helps get your sister 2-3 hours more sleep 3-4 days a week, perhaps that's sufficient for now. When school starts up, that should help - as you'll be sending him off to school before work, assuming he's starting kindergarten (if you're in the US). If you're not somewhere that school starts at 5, consider if there are options you have for public-assistance pre-schools.