KNRG,
First, there are a number of prior threads on Boulder and surrounding areas, so let me encourage you to search if you have not already (yes, I know the search is not what it used to be). If "Boulder" produces too many hits, try "Pearl" or "Flatiron." I know these threads exist because I've commented in a number of them. There is a lot of good information in them which may not be repeated in this thread.
Second, museums in Boulder will probably take part of a day, if you include Western Art and the race car museum (both near Celestial Seasonings); I think the race car museum has very limited hours. NCAR is worth a visit. The railroad museum east of Golden is good for an hour or so unless you're really into RRs. The motherlode of museums, etc. in the area is in Denver. Denver Museum of Nature and Science is pretty good, including a planetarium (CU also has a planetarium, but offerings may be sporadic). Nearby to Sci. & Nature is Denver Botanic Gardens, also worthwhile. Denver also has several art museums; the one with the most PR lately is the Denver Art Museum (aka DAM), in part due to the vertigo some people experience. I have not been to the Wings over the Rockies/Air and Space Museum. There are others as well.
Golden Gate and El Dorado Canyon State Parks are nearby and have a variety of trails for different skill levels. If you mentioned it, I didn't see what elevation you are coming from; if from a coast, you may want to spend a day or two in Boulder (about 5,300') before heading up to the mountains (Golden Gate SP is around 9,000' and Estes Park, mentioned above, is about 8,500', IIRC). Note: when driving around in the mountains, have some small bills with you, as some of the cities and state parks require daily fees for parking at trail heads, overlooks, etc.
On hotels, Boulderado which zdave mentioned is very close to Pearl Street. Boulder also has a full service Marriott, across the street from a newish open air mall, but a pretty good hike from the Pearl Street Mall. Outside of Boulder, when I stayed there several years ago before moving here, the Renaissance at Flatirons was a great hotel, and often had pretty good deals. It is between Boulder and Denver and a free shuttle ride away from the largest mall area north of Denver.
If I were you, I'd save Pearl St. Mall for a warm evening with your S.O. Most shops seems to stay open until 8 or 9 (a few later).
The area in or near Boulder has many good rock climbing areas. Also, there seem to be a lot of geocaching caches in the area. There are many walking, hiking, and biking trails in the area (and shops around which rent bikes). There is some tubing (riding an intertube in a stream) in Boulder depending on water levels, but whitewater rafting is as close as Idaho Springs (there is a thread discussing operators in I. S.). Also, some gold panning near I. S.
I hope those thoughts help. And I really encourage you to go back through similar threads in this forum. I think you will find enough to stay busy for a week. (And apologies if I repeated a comment someone elso posted.)