I like the idea of leaving a letter at least, or maybe a memento if there is anything you & your estranged son both liked or have a shared precious memory of. It's good that you plan to write your supportive nephew into your will as it's always nice to see things go to people who genuinely cared for the person who has died, as such. As my family is somewhat fractured it is hard to advise what to do about your estranged son, but I would consider not leaving him much if he doesn't care that you have had heart surgery whilst grieving and he couldn't be arsed to attend the funeral of his father or offer some moral support and/or practical help at what must've been a very difficult time for you.
I have a will, but am about to re-write it. My daughter cut all contact some years ago, and while I don't have anything of value to leave I just want to be clear if I come into any money, win anything of value, or any of my 'personal library' of books turn out to be worth a bomb that my long-term partner of 30 odd years would benefit. My mother remarried and she and her husband told me some years ago that their house(s), investments and money would be shared between my sister and my brother (their son, who I believe will inherit the bulk of it with my sister getting the rest) and that they had written me out of their will (that I didn't know I was ever in in the first place but hey ho!) I may write letters for my daughter, any grandchildren I may have, my (long-divorced) parents and my partner - good way to show feelings etc.
That said I am looking into starting to sell some of my possessions to put some money aside for my funeral. I don't want my partner to be stuck with costs on top of grief!
I hope you can decide what to do and live with your decision(s) - I also hope your nephew, and hopefully other friends or family continue to support you. Best wishes