Let's replace them with something more subterranean and/or some undead.
Agreed. If we keep the CR at 2 like the Dire Weasel, the SRD gives us a choice of...
Chokers or Scum?
Neither of those seem to be any use. Well, the Crypt Kobolds are a rung up the nastiness ladder compared to the regular variety, so let's try CR 3 Underground monsters, which are...
Derro, Ethereal Filcher, Gelatinous Cube, Grick, Phantom Fungus, Violet Fungus and Rust Monster.
If we cut out the mindless ones (Cube and Violet Fungus) and those too intelligent to be "attack beasts" (Derro and Ethereal Filcher) that leaves the Grick, Rust Monster and Phantom Fungus.
All those would make could "pets" for the Crypt Kobold. I've seen some scenarios with small humanoids siccing Rust Monsters on their foes, but it is a nasty tactic that I would rather reserve for special occasions rather than have all Crypt Kobolds use it. Besides, Rust Monsters wouldn't be of any help against foes which don't use metal.
A Phantom Fungus would seem problematic, since its
greater invisibility will work on the Kobolds too. If they put a collar on it to help them direct it into battle, then their enemies will be able to locate their pet too.
So that leaves the Grick. Another reason I lean towards the Grick is that it lives in groups of 1-4, implying it's a bit more social than the other two. Phantom Fungus are always solitary, and Rust Monsters can only form mated pairs, which implies they aren't good with company.
Besides, the
Monster Manual illustration of a Grick shows it crawling through what could be a crypt, while the Phantom Fungus's picture seems to show it in a subterranean Fungal Forest.
So, Crypt Kobolds with their pet attack Gricks?