To read reviews on Elk Meadows RV or Spruce Lake RV here's a site:
http://www.rvparkreviews.com/regions/colorado/estes-parkCall and ask how far it is to catch the shuttle. Yes, they're expensive and probably not a 'resort-type' atmosphere but you're only spending possibly two nights and you'll be gone a good deal of time so sometimes you have to make do.
Still consider staying IN the park though.
Here is Rocky Mtn. Nat'l Park's web site with lots of good information on things to do, road information, camping and the shuttle bus routes. Check it out thoroughly for help.
https://www.nps.gov/romo/planyourvisit/shuttle_bus_route.htmYour dog might hold you back from doing things in the national parks. Any chance of having a relative or neighbor taking it for this time?
If you haven't been to Mesa Verde Nat'l Park yet I would recommend doing that if you can work it in. If you can, the boys - and you - would love one of the ranger walks to the ruins. There's one that you climb ladders and crawl through a very short tunnel (6 or 8') to get from ruin to ruin. That would be fun depending on the boys' ages.
I really don't think the boys would get much out of Black Canyon unless you just do a drive through. From there you could take 50 south through Montrose and pick up 62 at Ridgway, then 145 south into Cortez and Mesa Verde.
You have a lot of options for this awesome state. Hope you can return and do more.