Check if the dealer sells them or try a junk yard.

 

Go to any dealer who installs roof racks on brand new V's and ask for those plastic covers. I'm sure they throw them away,, useless for them!. But very much important for you to prevent water inside that eventually rust the bolt and other.
I almost walked away from the dealer without them the day I picked up the new V.

 

You probably won't find any Honda CR-V (not evev a Gen 1) at a junk yard or a pick and pull because these cars are still running. The dealer probably does throw them out so I would check there first.

Or you can cruze a mall parking lot and borrow one off of another CR-V it is the easiest and most cost effective way but it can probably land you in jail. I would just go to the dealer.

 

Not sure what to call this other than 'cap'. I have a 2007 CRV that I bought used. On the roof rack trim, drivers side, near the front windshield there is an exposed nut and screw. There should be a black plastic piece that covers the screw and nut that is sort of shaped like a square.
Can anyone recommend where can I find the replacement part i.e. 'cap'?

I just bought a 2007 and I need the same plastic cover/cap! Wonder if someone "borrowed" it from the previous owner. I can only imagine what the dealer wants for this... not that I would go to find out

 

Update: I couldn't find this at any junkyard, but turns out the dealer sells this cover for only $6. Sold!