I am so sorry to hear this - so very hard.
When my DH died, my 4 year old GS was just the best person to have around. He was sad but real - he bobbed into my house shortly afterwards and I could hear him coming down the hallway shouting "I am so sorry Grandpa has died Grandma" and flung his arms round me, and proceeded to talk about DH - I cannot tell you how that helped me. Everyone else was trying so hard to say the right things, but he just came right out with how he felt; everyone else was mentioning him obliquely but wee GS just wanted to talk about him. He was openly sad, but he invited chat about the things we would remember - he would forget about it all and play happily, then suddenly want to remember something else. He talks about him lots and his emotions are very uncomplicated and quite refreshing.
I told him that Grandpa was gone now, but he would live on forever in our memories and in all the things he did with us - he accepted that without any problem.
It sounds as though your father's end of life was slow - and it was so for my DH. In a way I think that helped my GC - they had watched him gradually change from active Grandpa to someone confined to bed and needing help - they would take him drinks etc. and delighted in letting me know his "wee bag" was full! So in a way they were part of the gradual leave-taking.
Your son will be OK - and he will cope with you being sad - he cannot be sheltered from that, but needs to learn that it is a part of this life.
Take care, and take courage. Enjoy your memories together.