It should work, but may not be as much of a counter as you think
With the description of the spell as written, you should be able to cast it on a hostile, invisible target - so long as it is within range and you have a clear path, as you say.
However, keep in mind that 'spells do (only) what they say they do'. Just because the target is surrounded by a 'shimmering field' doesn't mean that their invisibility is negated. Compare the description from Shield of Faith with that from Faerie Fire. The latter spell also outlines the target with light, but explicitly says "the affected creature or object can’t benefit from being invisible." Since Shield of Faith does not say that, there is no reason to think that invisibility would be countered.
In particular, the invisible-and-now-shielded boss would certainly still receive the benefits of advantage on attacks on creatures that could not see it, and of being attacked at disadvantage because it could not be seen, as standard per the Invisible condition.
How noticeable the 'shimmering field' is would be open to DM interpretation - would it blur their edges when they were visible but be an almost unnoticeable distortion in the air when invisible during the heat of combat? Or would it amount to a glowing outline like faerie fire - obvious but not shedding light?
A generous GM might allow you to use the shimmering field when deciding 'what space to attack' when calling attacks on unseen opponents, and might adjust attempts for the shielded creature to Hide (adjusting their Stealth roll or their opponents' Perception rolls). But none of these allowances should be taken as given from the description in the spell itself, simply because it doesn't actually say that it does that.
