I got separated and divorced when my son was 4. If you're fighting, its better, trust me.
Sit down with your son( with your husband if possible, but only if he will be on the same page and NOT confrontational) and just say that Daddy is going to be staying somewhere else for a little while. I would not dwell on that aspect of it, at this time. If he asks why, just reassure him that it has NOTHING to do with him- Daddy and mommy just need to work on some things separately, is all.
The important thing here is to reassure your son that you BOTH love him very much and think he is a very good little boy. Remember- NO DETAILS- he does not need to know them and it can be tempting to confide too much. Just reinforce the positive and don't get into the whys any more than you have to at this point. That time will come later.
If your husband is agreeable, I would set up a specific time/day for him to see his son right now, to keep your little boy's schedule as continuous as possible. If there is something they usually do together like go to the park on Sunday, then KEEP DOING IT.
Or set up a new routine. The most important thing is to stick to it, just as you always do and let your son know. Your husband could say " Today is Sunday. Every Tuesday we go and throw the softball at the park after dinner. Tuesday is in 2 days and I will come to pick you up right after dinner and we'll go to the park, just like always." of course, only do this if you know he will be reliable and show up.
If his grandparents are in the area and aware of what's going on, enlist their help. Let them know that your main concern is keeping everything as smooth and sheltered for your son as you can and that you would appreciate their help to do that, out of love for their grandchild. Right now there may be bitter feelings, but later on, the grandparents on both sides will appreciate it if you make a point of keeping them involved in your son's life.
Same with preschool teachers or neighbors and friends that you feel comfortable sharing the details with. They don't need to know everything- just enough to help cushion your son from the situation. For him, the more familiar faces around, the better!
If you do end up getting a divorce or making your separation permanent, then I HIGHLY recommend you and your husband see a professional mediator to make all your son's custody and childcare and support arrangements.
Let attorneys handle the legal aspects of things, but a few sit-down meetings with a mediator and your husband and you will give you both a 'rule-book' to fall back on. It will allow you to set up a firm schedule of visits, holidays etc. not just for your convenience but so you have a solid plan to show your son to let him know where he will be and with which parent on certain days or events. That will mean a lot to him.
A friend of mine whose parents went through an ugly divorce where the fighting over the kids went on for years told me this: "It's never a good time for a child when their parents get divorced. But if you do it now, while your son is little, you can shelter him from the worst of it. And by the time he is old enough to start to see more things and be more observant , you will all have a 'system'. The system won't be perfect, but when you have parent-teacher conferences, or soccer games or other things to go to to support your son, you will all know how to be polite and smile at each other- you will all have the system down and he will know what to expect."
That advice was the best I was ever given about my son and getting divorced. It has proved to be 100% true. My son is 10 now- very bright, well adjusted and happy. He sees his dad every week, but has a wonderful relation with his stepfather and lives with us full time. We do not always agree about everything to do with my son- but we have the system and it works most of the time and we can all be civil and supportive of our son when we're together in public.
Good luck to you, however things work out. Please feel free to send me a message if you have other questions or I can offer any practical advice.