Wouldn't bother with Newquay, lots of much nicer small coastal villages around.
But yes, July is peak tourist season in Cornwall so def add journey time, especially into the tourist hot spots.
I agree eden project is hellish expensive, I've been on a locals pass but wouldn't have gone full price. Not sure how much small children would get from it, I think they're would need to be some organised activity on other than just the biome. Hot, walking up hill and plants probably won't inspire a 3yo.
You won't be far from pennywell. I've never been but looks good for kids
https://www.pennywellfarm.co.uk/
Cotehele (on a nice day the kids eould enjoy the parkland and gardens I expect)
Or Tavistock
anywhere on Dartmoor.
Around cadaver Bridge is very popular with families coming out from Plymouth as there is a car park, shallow bits of river for paddling and and ice cream van! No other facilities though. In July I'd advise aiming for hitting the popular areas on weekdays if you can.
Dartmoor zoo is just the other side of Plymouth.
Mount edgecombe has great grounds for walking around, doubt the kids would enjoy the house tour but there is lots of outside space.
Depending on your visit date then launceston agricultural show is on around the last Thursday of the month.
Smallish local 1 day show with animals etc (about 45 minutes).
Tamar trails is about 15miles away, has woods, cafe and toilets. Good if you have bikes
https://www.tamartrails.co.uk/kids/
And for low cost and low effort entertainment I've seen somewhere that they are revamping a couple play areas in saltash!