How old and heavy are your kids? Are you familiar with the practice of keeping your children rearfacing past a year?
I have a Honda Pilot. Not sure if you are looking new or used; mine is a 2006 and is fundamentally the same as '03-'08, with the '03 having a few minor differences.
The Pilot has a few really nice features. First, all six rear positions have lap-shoulder belts, headrests, and top tether anchors. From what I've read here, that's unusual -- especially the top tethers. There is LATCH second row outboard on both sides (so just two positions. I generally prefer the seatbelt, so that doesn't bother me too much, although I prefer LATCHable boosters so a third position *would* be handy.) The '09 and later models have three LATCH positions across the second row, and one in the third row.
The second row is also of ample width that you could likely seat your children three-across if you so wished - although I'm not sure about doing it with two Marathons plus booster. That may be do-able, but tight; it's possible you could do FF Marathon/RF Marathon/bosster of your choosing, but you might also need to put the Marathons outboard and get a narrower booster for the center.
As far as the third row, I'm not sure how you define functional. I can get three seats back there, but not without significant strife. Two seats would go back there easily. Its proportions are such that kids tend to fit the belts earlier than they do in most "normal" seats -- I watch a large-for-his-age 9yo who is just now borderline at fitting the second row (and most other) belts properly without a booster, but he fir well at 8 when I got the vehicle.
A bigger challenge is third-row access. There are a few ways around that; my favorite is to put rearfacers back there and load them through the hatch, but you could also leave the second row passenger seat open so that it could fold, or put a booster there that is easily removed for folding. There is no option for captain's chairs, at least not that I'm aware of.
All of that said, the biggest downside is space. With all three rows in use, I can't fit much in the way of luggage. I tend to say I can take people -- lots of them -- or stuff (both rear rows fold flat,) but not both. For my purposes, that works fine; I tend to either have the kids without luggage (nanny) or need space for luggage (recreation, trips, etc,) but not need to take more than five people, so I fold down a row and have tons of room. Although, I did drive on a chucch overnight a few months ago, and we were 7 people plus overnight luggage. It was tight, but we made it work.
Hope that helps. Feel free to ask any questions. There are lots of pics at the link in my sig -- that may help you visualize it as well.
