Listen, please...sad to say, there have been many cases where the mom didn't know the kids were being abused by the boyfriend/stepfather---and the moms didn't get into any trouble. Once the perv was out of their lives, the mom and the kids worked together to get their lives back in order. So...the thought of getting your mom in trouble should be the least of your worries.
As for going to the police---I'm not saying that you should put up being raped again so please understand that's not what I'm suggesting here. However, the best time to go to the police would have been as soon as possible after the rape occured. They would have gotten you to the hospital where a rape kit would have been used. The rape kit would have collected semen samples which would then get DNA tested. With DNA results, the perv couldn't deny what happened. Also, since you are underage, he couldn't even make the case that it was consensual.
Yes, your mom should know what happened. However, telling her while this perv is still living with both of you, may not be the best strategy. Not only could he deny it to your mom but you could face even worse consequences from him if your mom believes him.
Here's where it gets tricky. I do hope and pray that he doesn't hurt you again but if he does...be sure you don't bathe or in any way compromise the evidence. Also be sure to wear the same clothes you were wearing when the rape occured. Stay calm so as not to tip him off that you are going to the police. If you have a Cell Phone , take it with you and tell him that you are going out for a while (shopping, visiting a friend---whatever you need to say so you can get out of the house). Then calmly leave. When you get a good distance away, call the police. Tell them what happened and where you are. Preferably stand at an intersection on a busy street, if at all possible. If there are other people around, should he find you there he's not likely to cause a scene. When the police come, tell them to take you to a hospital so that a rape kit can collect evidence. No doubt, you will have to give a statement to a detective. Stress that you are afraid to return home while the perv is there. Also, let them know your concerns for your mother.
If you don't have access to a Cell Phone , then do one of the following: 1) If you know a nearby location where there is a pay phone, go there and call 911. 2) If there is someone you trust (a friend or neighbor) that lives nearby, ask if they will let you use their phone. 3) If you live within walking distance to the nearest police station, walk there.
It's very important that you go to the police. If he gets away with this, not only will he continue to harm you but he will also harm other boys. Also, if he is raping you and not using condoms, he is putting both you and your mother at risk for STDs.
Stay brave and know you're doing the right thing. The police or the hospital will give you and your mother referrals for counseling.
As a mother myself, I know that if I found out my child had been abused, I would have moved heaven and earth to protect my child. Trust that your mother feels the same way.
Also, please be aware that none of this is your fault!
My thoughts are with you. Best wishes as you work to get this perv locked up and out of both of your lives forever.