My youngest will be doing his first trip Friday night. I had planned on having him wear trail runner type shoes and just walk through the shallow creek like I would but am concerned his small size (33 lbs) won't really generate much heat even as much as he runs around. It should be almost 50 by the time we're there. I know he wants to play in the creek the next day but temps will only get up to mid 50s. Would I be better off just having him hike in his rain boots? I will have a dry set of sleep clothes to change into once we settle into the tent for the night.

Nobody with wild young boys?

Maybe a pair of lightweight water shoes for wading? Also, several pair of socks.

Crocs or rip offs for creeks and playing. Yes, it is extra weight. But they will appreciate it - and yes, little ones get very cold, very fast!
It also allows night time pee run shoes.