Under a strict - and in this case, I think correct - reading of the rules, I don't believe so.  A hybrid ranger can only use Hunter's Quarry "when you hit your quarry with a ranger power or a ranger paragon path power".  You're not hitting your quarry with a ranger power - you'd be hitting them with a seeker power.  In fact, I'm fairly certain that you couldn't even apply your Hunter's Quarry damage even if you just made a standard ranged basic attack with Clever Shot, as a ranged basic attack is not a ranger power.  That's the case with most hybrids - rogue hybrids can't sneak attack with a melee basic attack, fighter hybrids don't mark with a melee basic, and so on.  That's one of the weaknesses that a hybrid character accepts in exchange for the versatility.
As an aside, I assume that the way you're getting Clever Shot on a hybrid ranger is by taking the feat "Archery Mastery" that lets you drop a ranger at-will for one of the Expert Archer powers.  Because you can't normally choose Clever Shot in an at-will slot - it doesn't have a level.
All that said, yes, I do think that you can Clever Shot a Guardian Harrier attack, which does do some solid damage mixed with control.  Effectively, you've got an at-will that does 1W+Ability+mods, knocks the target prone, and can potentially do another Ability score mod worth of damage.  Solid, but probably a little low for a striker's bread-and-butter.  But great for a mixed controller/striker build.