If I activate Matsu-Tribe Decoy's ability targeting opponent's Trap Runner, can he activate Trap Runner's ability, blocking my creature, and making Trap Runner an illegal target for Matsu-Tribe Decoy's ability?
No. For this particular combination of cards, there is no time during which the Matsu-Tribe Decoy is a legal target for Trap Runner's ability.
The Oracle text for Trap Runner's ability says:
Target unblocked attacking creature becomes blocked. Activate this ability only during combat after blockers are declared.
Since this ability can only be activated after blockers are declared, Trap Runner would first have to block the Decoy... but then the Decoy is no longer an unblocked attacking creature.
Note also that your question asks about making the Trap Runner an "illegal target" for the Decoy's ability. Nothing about the Decoy's target being tapped (or otherwise unable to block) would make it an illegal target... just not one worth spending the mana on.