Assuming you have booked 2 seats (1 for yourself and the infant, the other one for your 3.5YO), I would select a middle seat for yourself + inf on the 787 and the window across the aisle for your 3.5YO.

On the 359, I would go for two middle seats, especially if you can get the bulkhead row, which you may be able to get due to your travelling with an infant. Or go for aisle + window again, again ideally in the bulkhead row if possible / available.

My wife and I find it easier to reach our young children across the aisle than trying to help them across the middle console, it’s just way less complicated, especially if you have to go into their seats for whatever reason.