We have stayed at the Boulder University Inn four times now and we have loved it each stay. I would recommend, hands-down, that you stay at the Boulder University Inn. Great service, great location.
If you have the option, get a room on the second floor otherwise you will hear every move the people above you makes.
If you stay here and have a hankering for fom late night food, Try DP Dough, Right next door, Open till 2am during the week and 3am on the weekends,
They have bikes you can use for free.
Great location for the price but feels a bit like the kinda place liquor store holdup dudes hide out in. A bit frayed and rough.