An Intellect Devourer gains the following benefit from its Body Thief ability:

While inside a creature, the intellect devourer has total cover against attacks and other effects originating outside its host.

The point of this is to find a viable solution to take out multiple Intellect Devourers quickly, from inside the host, while using as little consumable resources (such as Spell Slots or Items) as possible (or none).

The closest I have gotten, thus far, is trying to attack it with either Vicious Mockery or Sacred Flame. However, both

Vicious Mockery: You unleash a string of insults laced with subtle enchantments at a creature you can see within range. If the target can hear you (though it need not understand you), it must succeed on a Wisdom saving throw or take 1d4 psychic damage and have disadvantage on the next attack roll it makes before the end of its next turn.

and

Sacred Flame: Flame-like radiance descends on a creature that you can see within range. The target must succeed on a Dexterity saving throw or take 1d8 radiant damage. The target gains no benefit from cover for this saving throw.

both specify a necessity for you to be able to see the target. The quickest, easiest (but unviable..) "solution" I have, so far, is a Celestial Warlock with Pact of the Chain using a Bat or Pseudodragon familiar, choosing to see through its senses for its Blindsight, and then casting Sacred Flame at it.

This method is thwarted by the simple fact that (both via Twitter), while Jeremy Crawford has confirmed that blindsight qualifies for anything in the D&D rules that requires you to see something (as long as its within the radius), he has also confirmed that blindsight does not beat total cover. Meaning a working solution may be somehow sharing senses with a creature that has Tremorsense. Casting Beast Sense comes to mind, but I am unaware of any Beast-type creatures with Tremorsense.

Truesight does not detect an Intellect Devourer either.

You are going to have to see the Intellect Devourer.

As far as I know, sacred flame is the only spell that can get around total cover as most spells follow the targeting rules that state:

To target something, you must have a clear path to it, so it can't be behind total cover.

Sacred flame is able to ignore cover completely, but only because it is a specific exception to this general rule. Because sacred flame is the only option, you are going to need to find a way to see the intellect devourer.

Ghostly Gaze

From what I've seen, the only option to see directly into someone's skull is to use the warlock Eldritch Invocation Ghostly Gaze (found in Xanathar's Guide to Everything):

As an action, you gain the ability to see through solid objects to a range of 30 feet.

Once you can see into the victim's skull, you can call down holy light to burn it away (i.e. cast sacred flame).

Surgery

Credit to divibisan in the comments for this suggestion, and he is absolutely right. You could surgically add a hole in the host's skull (perhaps after knocking them unconscious via the sleep spell).

There was a procedure going as far back as ancient times called trepanning that involved boring a hole in a patient's skull. Remember that the host in question's brain is already eaten, so you aren't even really at risk of damaging the original host's brain. This would allow you to get sight on the Intellect Devourer to target it with sacred flame.

However, the Intellect Devourer would not have been affected by sleep, so at any time it might...

end... [the possession] as a bonus action

... and attack.

You can detect the Intellect Devourer using Detect Thoughts. However, you can't target it.

Detect Thoughts states (italics notes mine):

You can also use this spell to detect the presence of thinking creatures you can't see. When you cast the spell or as your action during the duration, you can search for thoughts within 30 feet of you. The spell can penetrate barriers, but 2 feet of rock, 2 inches of any metal other than lead, or a thin sheet of lead blocks you. You can't detect a creature with an Intelligence of 3 (Intellect Devourer has 12 INT) or lower or one that doesn't speak any language (Intellect Devourer knows Deep Speech & Telepathy).

Technically, an Intellect Devourer doesn't speak Deep Speech, and Telepathy is not really "speaking", but that's obviously not the intent of the spell.

However, the PHB states on page 205, in the chapter Spellcasting > Targeting:

A Clear Path to the Target

To target something, you must have a clear path to it, so it can't be behind total cover. If you place an area of effect at a point that you can't see and an obstruction, such as a wall, is between you and that point, the point of origin comes into being on
the near side of that obstruction.

This applies regardless of whether or not a spell requires you to see a target.

Geas

If you cast Geas on the Intellect Devourer before it enters the body (it cannot be targeted by Geas once it does), you can deal damage to it when it acts "in a manner directly counter to your instructions". Of course, this is a rather constructed example, since it takes one minute to cast Geas.

However, you could try to control an enemy politician by having a Geas'd Intellect Devourer teleport into its mind and telling the Intellect Devourer what to do. If it doesn't do so, it takes damage while inside a creature. Nevertheless, I don't think this is what you're looking for.

Arcane Archer's Piercing Arrow

The Ranger subclass Arcane Archer (XGtE, p. 28) has a Piercing Arrow feature:

Piercing Arrow. You use transmutation magic to give your arrow an ethereal quality. When you use this option, you don't make an attack roll for the attack.
Instead, the arrow shoots forward in a line, which is 1 foot wide and 30 feet long, before disappearing. The arrow passes harmlessly through objects, ignoring cover. Each creature in that line must make a Dexterity saving throw. On a failed save, a creature takes damage as if it were hit by the arrow, plus an extra 1d6 piercing damage. On a successful save, a target takes half as much damage.

One could argue that the sentence indicates that cover provided by creatures isn't ignored. However, that is neither RAW nor do I believe it is intended by the feature - considering that it otherwise also affects all creatures in that line, and taking the "theme" of the feature into account.

Wish

Needless to say, Wish can accomplish anything, but that's probably not what you're interested in either.

This feels like it may heavily come down to DM interpretation, but if you don't mind frying the host as well, another option might be the humble Fireball.

Fireball states that:

The fire spreads around corners.

This allows fireball to hit enemies in total cover so long as they are within the AoE of the spell and a path exists to the target (no hitting a target in a Resilient Sphere)

So, if the passageways of the ears/sinuses/whatever holes the Intellect Devourer made on the way in are not entirely blocked off, it could be interpreted as a series of tiny corners which the fireball is able to work its way around and through.