Yes the 4 Runners are significantly smaller. We had a 2016 4 Runner and when we found out we were due for our 2nd kid and I could not fit a rear facing car seat behind me (driver) and sit comfortable in the 4 runner, that was the ultimate decision to get a bigger vehicle. We now have two kids who are rear facing. We ended up selling it and getting a 2015 Expedition EL (we looked at Explorers, Suburbans, Yukons, etc.) and it has so much more room than the 4 Runner. It is amazing how much stuff we can fit in there, especially when the 3rd row is down. I can sit comfortably in driver seat and have a rear facing car seat behind me. We also have 2 dogs we take on occasion, so we are glad we got the EL in the end too. We figure the space behind with the 3rd row up is the same as the back of the 4 Runner (We did not have a 3rd row in the 4 Runner). So depending on your family size (if you have to deal with car seats and such) and how much stuff you have (Costco trips haha) I would look more into the Expedition. Having an actual 3rd row for more people to sit helps too. Another thing to consider is I felt like the 4 runner was completely gutless, even though it is rated for like 260 HP or something like that. But seriously felt like it could not get out of its own way, even my wife noticed it. I hated that from day 1 when we bought it new. Now driving a Ecoboost expedition, feel like we are in a rocket haha. The Expy also rides a lot smoother and quieter than the 4 Runner. As far as quality, never had an issue with the 4 runner in 2 years and the Expy seems to be good too from what I have read. Don't think you can go wrong either way in that area. The Expy gets about 1 mpg less than the 4 runner too. Not sure if you will need to use the vehcile to tow, but feel like the Expy will do better with that too.
We do miss the 4 runner for going to the dunes to get the family out on the sand, and up in the woods, snow etc though. It did awesome. We also loved the looks of the 4 runner too (not that the Expy looks bad) but our 4 Runner had a leveling kit, after market wheels and tires, blacked out emblems etc. and just looked good like that. We do miss that. The 4 Runner was very nimble on turning and fitting in tight places. Not sure how the Expy does in the snow and off road (if others may comment on that), but we arent going to take it up on fire roads in the mountains or out on the sand like we did with the 4 runner. Expy is lower, does not have the greatest off road tires on it right now and its Black! ha But will find out this winter with snowy/icy roads in town how the Expy does with the A4WD / 4WD.
In the end both are great rigs, I think the biggest factor is the room of the Expy and the power. So again depend on your family size/situation and what you ultimately want. We are very happy with the Expy and it was what we needed to fit our needs. If we could have we would have kept the 4Runner too! Sorry long reply but felt like we just dealt with same situation and can give you my honest opinion.