Every time we've gone we've rented HUGE cabins (for my husband's entire family-15 adults & 10 kids), so I can't give you any advice on that. We've always stayed in Island Park though. The only recommendations I have are for attractions & food. In West Yellowstone, I think that the Grizzly Discovery Center is fabulous. We happened to go when it was cloudy & overcast, with thunder rumbling in the distance. The wolves were howling at the thunder, and it was amazing! Also, since it was cooler, the wolves & bears were more active. They also have a time when the kids can be "junior bear handlers" (you have to be 7 I think) and before they let the bears out, they give the kids a bucket of frozen food & tell the kids to hide it under rocks, in fallen logs, etc. After all the kids are safely out, they let the bears out. It is fun to watch the bears search for the food. The kids especially get a kick out of watching a bear get the food they've stashed! I believe it was a bit pricey, but I thought it was worth it. They also have an IMAX theater there & the movies are usually really great too. I would suggest driving around Quake Lake & stopping at the visitor's center. It is neat too. Virginia City, MT is a fun old mining "ghost" town, but it is a little bit of a drive.
As far as in the park, we don't even stop at Old Faithful any more. It is WAY too crowded, and if you've seen it once, it isn't worth the wait & the crowds. Great Fountain Geyser was AMAZING, way better than old faithful. It was much taller, and lasted a lot longer. Also, there were only about 30 people watching it compared to the hundreds or so at Old Faithful. The waterfalls are also a must see for us, even Uncle Tom's Trail that has the 500+ stairs to the bottom of the falls. Two years ago, my daughter (then barely 3) walked the whole thing. I sat at the top though, since I was 37 weeks pregnant, and it was too hot for me. Norris Geyser Basin is a must see too. Mammoth is neat, but quite crowded, but you do get to see lots of elk milling around & munching on grass & leaves. We went to the north entrance last time & saw the Roosevelt Arch. It was neat too. The Lamar Valley is where you can (hopefully) spot some wolves and/or bears roaming aroung.
In West Yellowstone, Ernie's Deli is a fabulous place to get a "box lunch" to take into the park. Their sandwiches are huge (my husband & I usually share) & delicious. Arrowleaf is fabulous for ice cream too.
We usually go to Yellowstone every 3 years. We love everything about it except for the crazy amount of people & the stupidity of people. Make sure and bring lots of treats & snacks & to eat while in the park. Sometimes it is REALLY slow going on the roads. Also, bring extra water bottles and your patience!
Have tons of fun & make lots of memories!
Shellie