Well. let's see...
Boulder is not really in the mountains. It has access to lots of outdoor adventures but if you want to be IN the mountains, I wouldn't choose Boulder.
Estes Park is great, but my pick would be any or all of the mountain towns along the San Juan Skyway, which would include Telluride, Dolores, Durango, Silverton and Ouray. Keep in mind that the Telluride Bluegrass Festival is June 18-21 this year. That can be a plus or minus for Telluride that weekend.
Look at durangotrain.org for info on what they say is the country's longest, largest zipline adventure, if you are interested in that. Takes five hours to complete the whole thing!
One of my favorite mountain towns is Grand Lake. It's on the opposite side of Rocky Mountain National Park from Estes Park, and it doesn't get nearly the tourists that Estes does. There's still plenty to do if you like the outdoors-hiking, fishing, camping, horseback riding, etc. There are several great campgrounds and cabin options, as well as a few decent hotels. It's small and rustic and more "local", which I love.
I've lived in both Boulder and Durango and there are outdoor adventures both places. Boulder is much larger and as mentioned before, not in the mountains but right up against the foothills. Durango is in a valley surrounded by mountains and is much smaller.
If you are into rock climbing, biking, hiking Boulder may be a good choice. You would be within 1-2 hours of high mountains, fishing, Rocky Mtn National Park, while also near Denver.
If you want rafting, kayaking, fishing, horseback riding, jeeping and hiking, then Durango will fit the bill. Also Mesa Verde National Park is only an hour away.
If you want big mountains then you have to come to western Colorado. The San Juans cover more than 12,000 square miles, hundreds of them are over 13000 feet high, many over 14000 feet high. Most of this land is publicly owned so you can hike and camp and fish with freedom. The area around Ouray is called the Switzerland of America and Ouray is a charming town with wonderful natural hot springs. You can jeep into the back country for beautiful vistas and wildflowers, old ghost towns. Lots of things to see and do.
My vote goes to the "Little Switzerland of America," the San Juan Mountains above Durango. The narrow-gauge railroad between Durango and the old mining town of Silverton is spectacular! You mention lakes...are you going to do some fishing? Are you camping any? The Durango area has both. If you're interested in a mountain cabin, you might want to check out the Vallecito Lake area, 26 miles northeast of Durango. Boat rentals there also. We'
ve summered there often since the 60's. If interested, I can give you some specific places...semd me an E-mail for info.
Haviland Lake, about 18 miles north of Durango on US550, has great (yet primitive, i.e. no electricity, etc.)campsites overlooking the lake. "Usually" good trout fishing is to be had from the bank in summer. There is horseback riding at the turnoff to the lake if you have kids along, or are so inclined yourself.
Don't miss Mesa Verde National Park to the west while you are in the area. Have a great trip!
It wasn't included in any list so far, but since katemax said "etc." I'll add a few names. Steamboat Springs is definitely an outdoor place, though admittedly the mountains there can't compete with those in the SW part of the state. It's also hard to skip over Summit County -- Breckenridge, Keystone, etc. -- for outdoor activity of all types. And I guess Aspen would qualify nicely as well, if you can take yourself away from the diversions of restaurants, shops, music concerts, etc.
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