We did the drive between Sunriver and Crater Lake, and it took about 90 minutes. Sunriver is about 10 miles or so south of Bend, so the time depends on where you are staying.
I would not do the Lava Beds or anything in Bend first. Head straight down to Crater Lake, and yes, go early. The boat rides do sell out early. I would go early, go straight to the ticket office at Cleetwood Cove. If you do not get on a boat right away, you can go check out the lodge for a while and stop at the visitors center before your ride.
As far as the hike down to the boats, I can't remember exactly how long it took us to go down but we are hikers and based on other similar trails I would guess about 25 minutes. With your child being young, add a few minutes to that. It is a 700 ft elevation change, so many people take their time coming up.