I found my son in bed with his best friend (male) naked during a sleepover. I woke up at the middle of the night and went to go see if they were asleep and found them. What should I assume? Should I punish him and contact his friends family? I feel like a disappointment letting this happen in MY house. What should I do.
What should I do
As little as possible.
Since they are best friends, I assume there isn't a large age gap. So I think that whatever they were doing happened because both agreed to it, and was legal where you live. IMO, that's the most important thing to establish. If you have any doubt about this, you should intervene.
TL;DR: The important stuff
The important stuff, IMO, is:
To make sure that both boys stay safe. This means that if they're teenagers, they need to know about safe sex, and also about possible legal issues (e.g. in many countries, sexual acitivities among minors is okay as long as there isn't a large age gap, and most countries have age-of-consent laws to protect minors from abuse and eploitation).
Reassure your child that you're there for him and accept him and that your love isn't conditional on whether he likes girls or boys (or avoid a confrontation if him liking boys is a serious problem for you)
Respect your son's and his friend's wishes regarding how much they want to tell their parents about their preferred partners and activities in bed.
Now for the long answer. A lot of what it means to find them naked in bed depends on their ages:
If they're still pre-teens (say around 10 years old) then it's a fairly common thing, at least where I grew up, to be curious about other kids and "sex stuff" (sic - they don't actually know much besides it being taboo). It's why even younger kids invent games like "playing doctor". Kids aren't asexual beings and some fairly harmless exploration and experimentation won't hurt anyone. If you involve yourself, you'll make them both feel ashamed for no good reason, so I would let it go.
If they're young teenagers (say 13 or 14), finding them naked in bed doesn't necessarily mean that they're interested in the same sex (at that age some boys won't know for sure yet what their sexual orientation is, while others will, and they might still just experiment a bit before getting enough self confidence to talk to girls), but it's possible that at least one of them is or will turn out to be. If they didn't see you checking on them, again, I would not involve myself. But since at that age they might start to want to do more than look at and touch each other, you should find a way to breach the subject of safe sex with your son, to keep him safe.
Ideally, what I would also do is start dropping hints now and then that boys liking boys isn't a problem for you when an opportunity arises naturally (for example, if someone is discussing the topic anyway, or when you're watching a movie with a gay character etc), so your son knows that it's safe for him to come out to you if he does turn out to be gay.
(Obviously, if your son knows you caught him naked in bed, you don't need to hint - you can just tell him up front).
Of course this assumes that you're okay with having a son who might turn out to be gay, but if you're not, you'll have to come to terms with it. More and more research points in the direction that sexual orientation isn't anything you can willingly choose or change. Probably the best thing you can do in that case is to delay a confrontation.
If your son and his friend are older teenagers, I think it's likely that they are lovers and haven't come out yet.
In that case, again, make sure that your son knows about safe sex. Possibly your son hasn't come out to you because he isn't sure about your reaction; so, again, make sure he knows how what your view is so he knows whether he can safely come out to you. If he is gay and hasn't come out to you, this must be difficult for him and any help you can give him to make it easier will help.
The other parents
Should I punish him and contact his friends family?
I wouldn't involve the other parents if there was no legal reason to. It's bad enough to know your mom caught you and your best friend naked in bed, no matter what age they are; it's even worse to be told by your parents that your best friends mom caught you.
Don't run the risk of outing your son's best friend to his parents against his will. This strikes me as a horrible thing to do. If you feel you must talk to his parents, talk to the boy first so that if he is gay and his parents don't know yet, he can decide whether he wants to go ahead and tell them himself before you do it for him.
If you feel that the parents of your sons friend would hold you responsible for allowing a situation where minors might have been involved in sexual activities (or if this is actually illegal where you live), the way to avoid this happening again would be to talk to your son and tell him that he and his friend aren't allowed to be naked together in your house. But that will a) require that you involve yourself and b) result in your son and his friend doing whatever they're doing somewhere else. You can't watch them 24/7, so is this really better than knowing that whatever they're doing, they're doing in a safe place?
Or you could ask the other parents if it was okay with them, but again, if you do that, you should first talk to your son's friend. So if you really think you can't live with something like this happening again either in your house or your son's friend's house, you'll have to talk to both boys.
I feel like a disappointment letting this happen in MY house
I can understand that you're worried for your son and worried about what the other parents will think when they hear about this. But think about it. Why should you be? What, really, is so horrible about what happened? Why do you even consider punishing your son for it? What crime was committed in that bed?
Possibly, the incident signifies absolutely nothing, in which case it's hardly worth punishing. Possibly, your son and his friend are curious about sex, but not ready to involve girls, and trust each other to keep secrets. Possibly, your son is in love with another person and getting old enough to want to express that love sexually. Do you really need to punish someone for falling in love? Why would it be so horrible if your son fell in love with someone and expressed that love in the most secure place he knows, at home, in his room?
You seem to be feeling upset for letting something happen in your house you don't seem approve of. I suggest you reframe the way you're thinking about this: Whatever happened, you had no way of knowing about it beforehand and preventing it, and you won't be able to prevent it from happening again, though you might stop it happening in your house. Whether you approve of it or not, you can't change that both boys wanted it to happen, and if the boys want to do it again, they will, no matter whether you approve of it or forbid it.
But now that you know, I would look at it like a gift: It gives you advance warning that your son might one day want to talk to you about his sexual orientation, and it will allow you to help your son have this talk sooner, and make it go smoother, because it won't come as a surprise to you, if it does come. And if you get the feeling that your boy wants to talk to you, but can't get up the courage, you'll be able to help him along.
I know I'm basing all this on the premise that you don't think gay people are sinners, or go to hell, etc. It's possible that I'm wrong. If you actually do think that and can't accept a gay son now, DON'T force a confrontation now. You don't know for sure yet, so don't try to find out now. You won't be able to "change him back" if he actually is gay, and if you try, you'll make his life miserable because he'll either have to pretend to be someone he isn't to make you happy, or break with you. Instead, try to find someone you trust that's supportive of gay people and discuss this with them. This will be difficult for you, and it might take a long time for you to come to terms with it, but I don't think there's a way around it if you love your son.
Don't panic. It may or may not be an issue. The most important thing is to establish a strong relationship with your son. Being his mother will help because the subject is less confronting when it is the parent of the opposite sex talking.
Given he is a teen, it can be a confusing time and may just be a phase on the way to working out where on the range of behavior he is. It is better to underreact and build up your concern than overreact and drive a wedge between you.
He may feel annoyed that you were "checking" on him. Did you have any suspicions that led you to check on them or was it complete shock that happened because you were innocently just being mom?
Maybe open honestly with how you found out and then explain how others may see it, then take it gently from there.
Good luck, it's a tough one but may end up being a good outcome.