These have got both boys to the best of my memory without checking them, haven't included any that I know were primarily Dean.

Fangirls, UnSubs and Classic Cars
https://www.fanfiction.net/s/8446945/1/

The Deep Indigo Night
http://portraitofafool.livejournal.com/22046.html#cutid1
The prompt I claimed was: Criminal Minds/Supernatural, Sam Winchester, the BAU team, in the year that Sam hunted on his own or with the Campbells, he was willing to make several necessary sacrifices just to get his targets. The BAU follows his trail. How do the BAU profile a soulless man?

Fanning the Flames
http://archiveofourown.org/works/436415
Someone or something is going after fans of the Supernatural books. The BAU think it's a religious nut. Dean and Sam think it might be a restless spirit. Only one team is right.

Hunters and Prey
https://www.fanfiction.net/s/4929747/1/Hunters-and-Prey

Mask of Sanity (this is actually a stand alone story that is part of a larger series which is excellent!!!)
https://www.fanfiction.net/s/5479811/1/
Bodies in a small town bring the Criminal Minds team and the Winchester brothers into town, but with different missions. Strangers and Angels 'verse in the SPN fic world.

This Bitter Earth
http://archiveofourown.org/works/1171253
The Winchesters and the FBI's Behavioral Analysis Unit investigate the same case, a series of mysterious deaths on the grounds of a South Carolina plantation. Set late in the 4th season for both shows.

and this doesn't really have interrogation but has both boys and is a great crossover!

Feds, Felons and Pie
http://archiveofourown.org/works/3357020/chapters/7343108
It was just another case, until Spencer got cursed. Now he looks four years old and they have no idea who cursed him. Thankfully Spencer knows people.
Who you gonna call?
Winchesters!