If you really want to gate check both and you get a 'no' at the airport, you can always ask to talk to a complaint resolution officer. Airlines have to have these for any special assistance 'problems'. That would be THE person in the loop of what is possible. Kindly explain and ask him/her what is possible and what isn't. Sometimes -less then often in my experience- those working the check in don't know all of the rules and options. If the answer is no; OK. If it's yes, OK also.
I also had no idea that we could have asked for an aisle seat with a small chair. With our son being 6 (53lbs) that is going to come in handy for our next trip seeing that our plane is full. I never knew that was even an option and I have reading these boards through and though! That's a GREAT tip!!
Thanks!
You're welcome. With these things; talk to the airline. Name anything you might worry about or might run into. I'm confident that the airline would've mentioned the aisle chair themselves if you expressed worry about boarding. Heck, even what I call 'hellish airways' would've done that.
You're still in full parent mood, rightfully so with a young child. You grow 'into' the carrying. It creeps up on you. While the difference between a 3 and 4 year old isn't that much, if you keep thinking that for a couple of years? There you are, carrying a 6 year old that is now a lot heavier than 3 years ago. For these thing it can sometimes help to think about an adult in your sons situation. No way they could still be carried on board by loved ones.

How would they do...... (insert whatever you're wondering about)? There are services in place to take care of that, therefor they are also there if your son would need them. Keep in mind; you've got many more years to go. If it does become a "strain", it's better to safe your bodies for lifting him in situations where it's absolutely neccessairy and use services where available to make it easier on you guys.
If you ever need it; these aislechairs also are available on flights for transportation from seat to bathroom and vice versa. Not on the small planes but on the larger ones like Boeings, Airbusses etc; check. Not only is it a lot less strain on the body, if unsuspected turbulence hit, you'ld rather have son sitting down than you or DH carrying him and in worst case falling down.