Congrats on the twins!
I also have a 2yr old, and had twins about a month ago! I specifically got my 2013 SR5 w/3rd row to haul my kids around in something other then a minivan. (It was also a good excuse to get back in a 4runner!)
It looks like with the right seat combination, it is possible to put 3 seats across the 2nd row, however it looks pretty tight, and not all seats will be skinny enough to fit across. I have a Brittax Marathon 70, and two Grayco Snugride 35s. There is no way I could fit those 3 across.
My advice would be to bring your car seats to a dealer, and try to fit them to a 2 row model, and a 3 row model. I spent several hours at a dealer trying to figure out how to get all my seats to fit in a 4runner.
This is my seating configuration for my kids:
-The Twins in their Grayco Snugrides in 2nd row (one on each side, middle open)
-The 2year old in the 3rd row pass side (No LATCH Back There so attached by belt)
*Carseats are saftey tested using seatbelt attachments, and LATCH actually has a weight limit where they are no longer safe, so using the seatbelt to attach is not a saftey risk.
I leave the pass side 3rd row seat down so I have some storage (not much, but good thing I am good at tetris!) With carseats in the 2nd row, you can't access the 3rd row from them. I will be getting my 2yr old in and out via the hatch, which is actually easier then accessing the 3rd row from the 2nd row.
Getting my kids in and out of the 4runner isn't super practical, but it isn't bad. Sure a minivan would be more logistically practical for kid hauling, but I can't see myself paying 30k for a minivan that I will hate, when for about the same price I can have a 4runner, which I love. When you have 3 kids in carseats, your vehicle options become extremely limited.
Also:
http://www.toyota-4runner.org/5th-gen-t4rs/62407-infant-seats-4runner.html#post521788