If you just dropped the cap into the bowl and it floated out of reach "toward" the pump base...then you shouldn't have pulled it up into the pump. In that case it has moved along and is just below the toilet bowl but "out of reach"; i.e., it just moved horizontally.

If you have pulled it "up" into the pump, then it may be in the cylinder (that's veritcal).

If you pumped it through the back of the toilet into your waste line hose, then that's a different story.

Where is the cap? When did you stop pumping. etc?

THe original thought that you just lost the cap before the pump and below the bowel led to my suggestion for a wet dry vac; If you need to pull the head pump apart, then use the wet dry vac and just proceed like you're rebuilding or lubing the pump.

If you have pushed this cap into your hose after the head pump and you aren't sure whether its going to jam that up, etc., then you have a different set of issues.