I actually just read about this type of situation recently. Unfortunately, there's not much you can do at this point except hope that you find that other passengers are open to switching seats, which isn't guaranteed because people obviously choose aisle and window seats on purpose.
Of course, their other option is to babysit your kids for the entire flight... so they might be more willing to adjust.
The advice I read wasn't all that helpful - purchase priority seating/pay to choose your seats when you book your ticket.
Personally, I think that's entirely unreasonable. A family with young children shouldn't have to pay more just to get seats next to each other. My thoughts are that if children are young enough to be unable to travel on their own (without an airline employee escort) then they should be considered too young to be separated from their parents during a flight.
To encourage the other passengers to change seats (especially for the 3 year old) I'd probably start giving instructions on what to... where his snacks and toys and drinks are, what drink to order for him when the beverage cart comes by, how to get him to take a nap, etc. =D I'd be interested to know how long it would take the other passengers to be willing to give up their seat to avoid babysitting. And, ultimately, it's not your issue IMO, it's the airlines' issue and they can take it up with the airlines.