Sounds like somewhere a while back the dynamics of your family changed in such a way that your son views you as a fellow sibling...not his mom. And now that your mom is gone, your sis has stepped into the matriarch role in your family.
Since we aren't there, we will never know if there is any hard truth to your sister's harsh criticisms, or if her judgements are totally off base because of the pecking order that has developed in the family (between you, sis, son and your deceased mom).
At this point of the game, you may never regain an authoritative role with your son, but I do believe you deserve his respect as his mother. And I do believe with family counseling, you might be able to achieve this so you can have a healthier relationship with your son during his fast approaching adult years.
I say your feelings are warranted and valid. You missed out on some special and important times with your son because of circumstances beyond your control. Don't stuff the feelings, just accept them for what they are. You're mourning for the relationship you never had with your son because you were too young and not emotionally and probably not financially ready for it. And now, your family isn't recognizing how far you have come or how much you've grown and are refusing to relinquish their parenting roles so you can rightfully assume yours.
When you calm down, and feel better a few days or weeks from now, approach your sister and ask her to join you and your son for family counseling. Tell her you are ready to be your son's mother and ready for her to start respecting your role as his mother. Say you want her to remain an important part of your lives, but her interference is slowing the healing and much needed growth between you and your son.
Hopefully she will respect that and join you. If not, it may be time to sever ties and move on.
Yes, motherhood is difficult. But you'll have a much better time connecting with your teen son without her having full access to your lives. If she can not respect boundaries, and will not go to counseling, you should go on your own before time runs out. He will be leaving home in no time, and you really don't want things to get to a point where you have no relationship with him in the future.