I recommend you think carefully about age-appropriate activities. I don't know your son's interests or capabilities, but consider mine: I have loved the outdoors and natural scenery for most of my life, but only since about age 8. Prior to that I had little patience for things that merely could be seen. And I was precocious compared to my peers at that age. A boy of 5 years is mostly focused on things he can touch and do. To that extent, he'll probably form more memories of climbing on the statues of animals such as the desert tortoise and bighorn ram at the Arches Visitor Center than any of the arches, windows, or balanced rocks he sees in the park.

That said, I'll offer a few suggestions about each park:

Arches is a small park and is all about the hiking. There are no offroad vehicle trails. You can see a fair amount from the paved roads and pullouts, but taking even a short hike opens up a lot more. I'd suggest sticking to the shortest trails and letting your son climb around on the rocks. And definitely plan to spend time on the statues of the desert tortoise and the bighorn ram at the visitors' center.

Canyonlands is a much more expansive park and basically requires some form of transportation. Teens might get a huge kick out of renting mountain bikes and biking the White Rim trail. With a young boy you should stick to driving, as his energy may give out at any point. And for that same reason, renting a vehicle yourself might be better than taking a guided tour. Otherwise, what if your son decides 45 minutes into a 4 hour group tour that he's bored, tired, unhappy, etc? There are several outfitters in town where you can rent a Jeep and go off on your own.